[aroma.affymetrix] Re: cant get aroma to load

[Pierre Neuvial]

Thanks for reporting. Retry with:

   if (.Platform$OS.type == "windows") options(url.method = "libcurl")
   source("https://callr.org/install#aroma.affymetrix;)

We've updated the online installation instruction accordingly.

On Thursday, October 31, 2019 at 6:06:43 AM UTC+1, Sreya Mukherjee wrote:
>
> i get the following error. please help
>
> *source('https://callr.org/install#aroma.affymetrix 
> ')*
> *Error in file(filename, "r", encoding = encoding) : *
> *  cannot open the connection*
> *In addition: Warning message:*
> *In file(filename, "r", encoding = encoding) :*
> *  cannot open URL 'https://callr.org/install#aroma.affymetrix 
> ': HTTP status was '400 Bad 
> Request'*
>

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Re: [aroma.affymetrix] Dealing with batches

[Pierre Neuvial]

Dear Peter,

First, just to make sure we are talking about the same things, when
you write "I have applied ASCRMA to each array separately.", you mean
that you applied ASCRMA(v2) to each of the two *batches* separately,
right ?  In the aroma-project world, we usually reserve the word
'array' for what you called a 'sample'.

Then, let me recall or clarify that ASCRMA(v2) processes each or the
28 samples separately.  Therefore, it would make no difference you
applied ASCRMAv2 on a single data set of 28 samples, or to two
separate data sets, ...or to 28 separate data sets.  This is why
ASCRMA(v2) is called a "single-array" method.

>From the density plots, it seems to me that the normalization was able
to make the intensity distributions more similar, which is a good sign
that part of the experimental variability has been removed.  However,
I would like to emphasize that we do not expect these distributions to
be strictly identical after normalization (as would be the case if we
were performing quantile normalization).  In fact, some of the
differences we see after normalization may correspond to true
biological signal.

At first sight it seems to me that it is safe to use your normalized
data for downstream analysis.

If you want to dig further, one thing you could do is to plot these
densities for the normal samples only.  There, we do not expect much
biological variation in the densities.  If there is still clear
variation between the two batches, then one possibility to reduce it
could be to force the "average" density of the normal samples of the
two batches to be identical.  The transformation used for the normal
samples of each batch could then be used to normalize the other
samples of that batch.

I hope this will help you.

Best,

Pierre



On Tue, Jan 5, 2016 at 7:32 AM, Peter Savas  wrote:
> Dear Group,
>
> I have 28 samples of tumour normal pairs, run on 2 GenomeWideSNP6.0 arrays
> several months apart. Some of the pairs have members on different chips (ie
> tumor on one, normal on the other). I am not sure about the best way to
> normalise the data such that these split pairs can be used for downstream
> analysis. The plan is for ASCRMA, TumorBoost and then PSCBS.
>
> I have applied ASCRMA to each array separately. Probe density plots pre and
> post this normalisation are attached. It seems that there is still some room
> for improvement.
>
> Thank you and all the best for the new year.
>
> Regards,
> Peter
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
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>
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Re: [aroma.affymetrix] Cannot fit normalization function to enzyme error

[Pierre Neuvial]

Hi Z.,

If you want people to be able to help you out, then you need to
explain exactly what you did.  Can you report the output of
sessionInfo() and traceback(), and post a complete code example ?

Have you checked that your problem is not already solved in the other
threads titled Cannot fit normalization function to enzyme ?
You can find a few of these threads by googling this error message.

Best,

Pierre

On Tue, Jan 21, 2014 at 7:34 PM, Z. Ding dingposit...@gmail.com wrote:
 Hi,

 I got this “Cannot fit normalization function to enzyme, because there are
 no (finite) data points in argument 'y'.” error from doCRMAv2, for 2 SNP6
 files, out of 150+ samples. A colleague run the same set of SNP6 CEL files
 which caused this error without any problem, He used the same latest version
 R as I did, on same/similar servers.

 Have you seem this error? It would be a great help if you can tell me what
 might had caused it. Especially, how to resolve it!

 Thanks!

 Z.


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Re: [aroma.affymetrix] Basic manual

[Pierre Neuvial]

Hi,

You can start by the website of the Aroma project:

http://www.aroma-project.org/

In particular, see the get started tab on the left.

Pierre


On Thu, Jan 16, 2014 at 2:20 PM, Fernando Andrade fernand04ndr...@gmail.com
 wrote:

 Hello, this is my first time using aroma.affymetrix, and I'm having many
 troubles. Is there a manual covering the basics about aroma? Like
 explaining which analyses can be done and the files nedded for each of them.

 Thanks

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 latest version of the package, 2) to report the output of sessionInfo() and
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Re: [aroma.affymetrix] smoothing after CRMAv2 and before CBS?

[Pierre Neuvial]

Hi Emilie,

It's certainly possible to do this within the Aroma framework (e.g. using
the function binnedSmoothing).  It's probably not as straightforward as
running the segmentation directly, though, because this is not a typical
use case.

In fact, I'm not sure why you want to perform smoothing before segmentation
?  Smoothing is definitely not required before segmentation, and I would
actually discourage to go this path because it will end up in a loss of
resolution along the genome at the smoothing step.

Best,

Pierre


On Tue, Dec 3, 2013 at 8:53 PM, Emilie emilie.lalo...@gmail.com wrote:

 Hi there,

 I'm new to processing Affy SNP6 chips and so am mainly experimenting with
 different methods to date. I ran CRMAv2 and followed steps 1-4 from the
 vignette (http://aroma-project.org/vignettes/CRMAv2). For step 5, I want
 to do a paired analysis.

 Previously I've used DNAcopy to perform CBS for other array types, and
 would like to follow a similar procedure, which includes smoothing prior to
 segmentation. Is this possible using the aroma.affymetrix package? So far
 I've followed the vignette for paired CNA analysis (
 http://aroma-project.org/vignettes/pairedTotalCopyNumberAnalysis) but
 haven't seen any options for smoothing.

 thank you very much,

 emilie

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 latest version of the package, 2) to report the output of sessionInfo() and
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Re: [aroma.affymetrix] Re: Setting up annotation data in aroma.affymetrix

[Pierre Neuvial]

  in a
  directory of format:
 
annotationData/chipTypes/chip type/
 
 
  and  my   location  is
 
 
  C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/chipType/HG-U133_Plus_2
 
  i just  creat new folder in annotation data with name chip type and
  inside
  it  another folder with chip name ???
   iam just  confused  ??

 What you're missing in Aroma.affymetrix searches for CDF files in the
 annotationData/ directory of the current working directory is the
 part that says ***of the current working directory***.  In other
 words, in your current working directory (i.e. getwd()) you should see
 subdirectory annotationData if you call list.files().  You may find
 the following page useful too:

   http://aroma-project.org/troubleshooting/DirectoryStructures



 Also, I strongly recommend to put your data files (annotationData/,
 rawData/, etc.) somewhere else than where R installs packages.  Right
 now you seem to place them in:


 C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/chipType/HG-U133_Plus_2

 The directory 'C:/Users/nwayyin/Documents/R/win-library/3.0/' is where
 R install packages and you shouldn't add/remove things from there.
 For instance, if you uninstall aroma.affymetrix then all your data may
 disappear as well.  Instead, let your working directory be something
 like:

   C:/Users/nwayyin/AromaAnalysis/

 and let that be your working directory in R.

 /Henrik

   why this error occur  please  if  you know  the  cause of  problem
  please
  tell me
 
 
  On Tuesday, April 30, 2013 3:16:00 PM UTC+1, Pierre Neuvial wrote:
 
  Hi,
 
  Quoting myself,
 
  1. Read carefully the setup page:
  http://www.aroma-project.org/setup,
  and follow the links in that  page.
 
  The first link Location of annotation data files explains where
  annotation data files should be located.
 
  Best,
 
  Pierre
 
 
  On Tue, Apr 30, 2013 at 2:10 PM, nawin MOHAMMED naw...@gmail.com
  wrote:
  
   i  also  down load the CDF  from affymetrix  but its not working
   same
   problem
  
   Error: Failed to create AffymetrixCdfFile object. Could not locate
   an
   annotation data file for chip type 'HG-U133_Plus_2' with tags
   'full' and
   with filename extension 'cdf'.
   cdf - AffymetrixCdfFile$byChipType(HG-U133_Plus_2,tags=full)
   [2013-04-30 13:08:07] Exception: Failed to create AffymetrixCdfFile
   object.
   Could not locate an annotation data file for chip type
   'HG-U133_Plus_2'
   with
   tags 'full' and with filename extension 'cdf'.
  
 at #03. byChipType.UnitAnnotationDataFile(static, ...)
 - byChipType.UnitAnnotationDataFile() is in environment
   'aroma.core'
  
 at #02. byChipType(static, ...)
 - byChipType() is in environment 'aroma.core'
 - originating from 'text'
  
 at #01. AffymetrixCdfFile$byChipType(HG-U133_Plus_2, tags =
   full)
 - AffymetrixCdfFile$byChipType() is local of the calling
   function
  
   Error: Failed to create AffymetrixCdfFile object. Could not locate
   an
   annotation data file for chip type 'HG-U133_Plus_2' with tags
   'full' and
   with filename extension 'cdf'.
   getwd()
   [1]
  
  
   C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/chipType/CD_hgu133a2_libraryfile
  
  
  
   On Tuesday, April 30, 2013 8:40:35 AM UTC+1, Pierre Neuvial wrote:
  
   Hi,
  
   Please create a new thread (with a relevant subject line) instead
   of
   replying to an unrelated one.
  
   See below.
  
   On Tue, Apr 30, 2013 at 9:22 AM, nawin MOHAMMED naw...@gmail.com
   wrote:
   
   
Greeting  ,
   
iam  a Phd student , i  try implement aroma package but its not
working
with
me , i don't know where is the error,   and  i  have question
the
shiptype
folder  is not exist be default  in annotationdata,  i  just
create
a
folder in annotation data name it chiptype and i put the cdf
file in
it
, is
that possible ???   please  i need your advice this is my
program
   
   
   
  
   Yes, that's what you should do.  Here is some general advice that
   could save you lots of time:
  
   1. Read carefully the setup page:
   http://www.aroma-project.org/setup,
   and follow the links in that  page.
  
   2. Be really careful with the folder and file names:
   annotationData
   is not the same as annotationdata, etc.  The same holds for
   function
   names in the code you have pasted below, for example
   AffymetrixcdfFile is not the same as AffymetrixCdfFile, etc...
  
   3. Do not try to guess/invent code lines if you are not familiar
   with
   the aroma framework.  Instead, try to reproduce a vignette, for
   example this one:
   http://www.aroma-project.org/vignettes/GeneSTArrayAnalysis
  
   Best,
  
   Pierre
  
getwd()
[1]
   
   
   
C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/ChipType
ChipType(HG-U133_Plus_2)
Error: unexpected symbol

Re: [aroma.affymetrix] Errors when processed Vignette:CRMAv2

[Pierre Neuvial]

Hi,

This thread should help you solving your problem:

https://groups.google.com/forum/?fromgroups=#!topic/aroma-affymetrix/S_wLLGcU8S0

Cheers,

Pierre

On Fri, Jan 4, 2013 at 6:58 PM, Foxchase jianming@gmail.com wrote:
 Dear Henrik,
 I'm trying aroma.affymetrix for Affy's Affymetrix Mouse Diversity Genotyping
 Array. I made the arom annotation files using Affy's na32's NetAffx files.
 I use a public data 'GSE27691. Attached is the R history file.
 When I followed the Vignette:CRMAv2 I got error at the step: cesN -
 process(fln, verbose=verbose):

 cesN - process(fln, verbose=verbose)
 20130104 12:05:43|Normalizing set for PCR fragment-length effects...
 20130104 12:05:44| Identifying SNP and CN units...
   types
 1   2   5
24  626135 1832538
 20130104 12:05:44|  subsetToUpdate:
int [1:2458673] 25 26 27 28 29 30 31 32 33 34 ...
 20130104 12:05:44| Identifying SNP and CN units...done
 20130104 12:05:44| Retrieving SNP information annotations...
   UflSnpInformation:
   Name: MOUSEDIVm520650
   Tags:
   Full name: MOUSEDIVm520650
   Pathname: annotationData/chipTypes/MOUSEDIVm520650/MOUSEDIVm520650.ufl
   File size: 9.38 MB (9834930 bytes)
   RAM: 18.76 MB
   Chip type: MOUSEDIVm520650
   Number of enzymes: 2
 20130104 12:05:44| Retrieving SNP information annotations...done
 20130104 12:05:44| Identifying the subset used to fit normalization
 function(s)...
int [1:2292403] 25 26 27 28 29 30 31 32 33 34 ...
 20130104 12:05:44| Identifying the subset used to fit normalization
 function(s)...done
 20130104 12:05:44| Shift: 0
 20130104 12:05:44| onMissing: median
 20130104 12:05:44| Array #1 of 7 ('GSM685813')...
 20130104 12:05:44|  Reading and filtering fragment lengths...
 20130104 12:05:44|   Reading fragment lengths...
 UflSnpInformation:
 Name: MOUSEDIVm520650
 Tags:
 Full name: MOUSEDIVm520650
 Pathname: annotationData/chipTypes/MOUSEDIVm520650/MOUSEDIVm520650.ufl
 File size: 9.38 MB (9834930 bytes)
 RAM: 18.76 MB
 Chip type: MOUSEDIVm520650
 Number of enzymes: 2
 20130104 12:05:46|Summary of non-filtered fragment lengths:
  int [1:2458673, 1:2] 2744 2744 2744 2744 2744 2744 572 572 572 572 ...
V1   V2
  Min.   :7Min.   :7
  1st Qu.:  6161st Qu.:  542
  Median : 1149Median :  999
  Mean   : 1623Mean   : 1478
  3rd Qu.: 21983rd Qu.: 2002
  Max.   :32767Max.   :32767
  NA's   :233634   NA's   :233634
 20130104 12:05:46|   Reading fragment lengths...done
 20130104 12:05:46|   Filtering fragment lengths...
 20130104 12:05:46|   Filtering fragment lengths...done
 20130104 12:05:46|  Reading and filtering fragment lengths...done
  V1   V2
Min.   :7Min.   :7
1st Qu.:  6161st Qu.:  542
Median : 1149Median :  999
Mean   : 1623Mean   : 1478
3rd Qu.: 21983rd Qu.: 2002
Max.   :32767Max.   :32767
NA's   :233634   NA's   :233634
int [1:2292403] 1 2 3 4 5 6 7 8 9 10 ...
   UflSnpInformation:
   Name: MOUSEDIVm520650
   Tags:
   Full name: MOUSEDIVm520650
   Pathname: annotationData/chipTypes/MOUSEDIVm520650/MOUSEDIVm520650.ufl
   File size: 9.38 MB (9834930 bytes)
   RAM: 18.76 MB
   Chip type: MOUSEDIVm520650
   Number of enzymes: 2
 20130104 12:05:47|  Setting up predefined target functions...
 20130104 12:05:47|   Target type: zero
 20130104 12:05:47|  Setting up predefined target functions...done
 20130104 12:05:47|  Getting cell matrix map...
 'UnitGroupCellMatrixMap' int [1:2458673, 1] 25 26 27 28 29 30 31 32 33
 34 ...
 20130104 12:05:48|  Getting cell matrix map...done
 20130104 12:05:48|  Getting theta estimates...
 20130104 12:05:49|   Thetas:
 num [1:2458673, 1] 1047 477 3533 3499 3353 ...
 num [1:2458673, 1] 1047 477 3533 3499 3353 ...
   V1
 Min.   :  -143
 1st Qu.:  1785
 Median :  4562
 Mean   :  6687
 3rd Qu.:  9142
 Max.   :199787
 20130104 12:05:49|  Getting theta estimates...done
 20130104 12:05:49|  Calculating total signals...
 20130104 12:05:49|   Total thetas:
 num [1:2458673] 1047 477 3533 3499 3353 ...
 20130104 12:05:49|  Calculating total signals...done
 20130104 12:05:49|  Normalizing log2 signals...
 20130104 12:05:49|   Log2 signals:
 num [1:2458673] 10 8.9 11.8 11.8 11.7 ...
 [2013-01-04 12:05:50] Exception: Cannot fit normalization function, because
 none of the units are on fragments from a single enzyme, or equivalently,
 there exist no rows in argument 'fragmentLenghts' that only have one finite
 value.
   at #04. normalizeFragmentLength.default(y, fragmentLengths = fl,
 targetFcns = targetFcns,
   subsetToFit = subset, onMissing = onMissing, ...)
   - normalizeFragmentLength.default() is in environment
 'aroma.light'
   at #03. normalizeFragmentLength(y, fragmentLengths = fl, targetFcns =
 targetFcns,
   subsetToFit = subset, onMissing = onMissing, ...)
   

Re: [aroma.affymetrix] Error in getGenomeInformation

[Pierre Neuvial]

Hi,

The error message says: Failed to retrieve genome information for
this chip type: GenomeWideSNP_6

From your reply to my message in your other thread Problem with
AffymetrixCelSet cmd it looks like you are indeed missing annotation
files.  (Currently you only have the cdf, which basically connects
each location on the microarray to the corresponding probe idea; but
you don't have any information on the location of the probes on the
genome, which is why you get the above error message.)

Try to follow the CRMAv2 vignette:
http://aroma-project.org/vignettes/CRMAv2 step by step.  In the
Setup section of that vignette you will find how to get the other
annotation files.  And then your analysis should work properly.

Note that the 'doCRMAv2' block is essentially a wrapper that executes
the preprocessing step described in more detail in the above vignette.

Cheers,

Pierre

On Mon, Jun 18, 2012 at 10:58 PM, NT_CMU nitesh.tur...@gmail.com wrote:
 Hi

 I'm trying to run the command doCRMAv2, and i get these errors. Let me
 know what the problem is, if any of you have encountered this before. I
 thought i did not have some library installed but, i have both ACNE and
 aroma.affymetrix working properly.

 ds - doCRMAv2(LeeAV_2012,chipType=GenomeWideSNP_6,Full)
 Error in getGenomeInformation.AffymetrixCdfFile(cdf) :
 [2012-06-18 16:55:10] Exception: Failed to retrieve genome information for
 this chip type: GenomeWideSNP_6

   at #12. getGenomeInformation.AffymetrixCdfFile(cdf)
           - getGenomeInformation.AffymetrixCdfFile() is in environment
 'aroma.affymetrix'

   at #11. getGenomeInformation(cdf)
           - getGenomeInformation() is in environment 'aroma.affymetrix'

   at #10. getSubsetToAvg.AllelicCrosstalkCalibration(this)
           - getSubsetToAvg.AllelicCrosstalkCalibration() is in environment
 'aroma.affymetrix'

   at #09. getSubsetToAvg(this)
           - getSubsetToAvg() is in environment 'aroma.affymetrix'

   at #08. getParameters.AllelicCrosstalkCalibration(this)
           - getParameters.AllelicCrosstalkCalibration() is in environment
 'aroma.affymetrix'

   at #07. getParameters(this)
           - getParameters() is in environment 'R.rsp'

   at #06. process.AllelicCrosstalkCalibration(acc, verbose = verbose)
           - process.AllelicCrosstalkCalibration() is in environment


 Thanks

 Nitesh

 --
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 version of the package, 2) to report the output of sessionInfo() and
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Re: [aroma.affymetrix] Error when Creating binary data files containing copy number estimates (Agilent HG-CGH-244A)

[Pierre Neuvial]

Hi,

On Wed, May 16, 2012 at 9:05 PM, sean nj njs...@gmail.com wrote:

 Hi,

 I did get rid of the error message when I ran :

      unf - TextUnitNamesFile$byChipType(chipType)

 I got this done by loading the aroma.affymetrix package, in addition to 
 aroma.core.

 But now I got another error message when I followed Henrik's code at 
 http://aroma-project.org/node/88

 I was trying to creating data files containing log2 CN ratios. Everything was 
 fine until I ran

  units - indexOf(unf, unitNames)
 Error in indexOf.UnitNamesFile(unf, unitNames) :
 [2012-05-16 14:53:18] Exception: If specified, argument 'pattern' must be a 
 single string. Did you mean to use argument 'names'?
   at #02. indexOf.UnitNamesFile(unf, unitNames)
   - indexOf.UnitNamesFile() is in environment 'aroma.core'
   at #01. indexOf(unf, unitNames)
   - indexOf() is in environment 'R.filesets'
 


From the error message (pretty explicit) it looks like you should  have done

units - indexOf(unf, names=unitNames)

instead of

units - indexOf(unf, unitNames)

That's what you do below.

Cheers,

Pierre

 The command ran successfully when I tried to get units for certain probes

  units - indexOf(unf, names=c(A_16_P15025341,A_16_P00013121)
 + )
  units
 [1] 1006 1019
 
 I tried   ?indexOf.UnitNamesFile()   and here is what I got:

     indexOf(this, pattern=NULL, names=NULL, ...)

     Arguments

  pattern    A pattern to be used for identifying unit names of interest. If 
 NULL, no regular expression matching is done.



 names    Names to be match exactly to the unit names.

 ...    Not used.


 What did I do wrong?

 Thanks a lot for the help!

 Ying

  sessionInfo()
 R version 2.15.0 (2012-03-30)
 Platform: x86_64-pc-mingw32/x64 (64-bit)
 locale:
 [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252
 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
 [5] LC_TIME=English_United States.1252
 attached base packages:
 [1] stats graphics  grDevices utils datasets  methods   base
 other attached packages:
  [1] aroma.affymetrix_2.5.0 affxparser_1.28.0  aroma.apd_0.2.2    
 R.huge_0.3.0
  [5] aroma.core_2.5.0   aroma.light_1.24.0 matrixStats_0.5.0  
 R.rsp_0.7.5
  [9] R.filesets_1.1.5   digest_0.5.2   R.cache_0.6.2  
 R.utils_1.12.1
 [13] R.oo_1.9.3 R.methodsS3_1.2.2
 loaded via a namespace (and not attached):
 [1] tools_2.15.0
 


 On Tue, May 15, 2012 at 12:38 PM, sean nj njs...@gmail.com wrote:

 Hi guys,

 I was following the Vignette: Creating binary data files containing copy 
 number estimates and trying to work on agilent HG-CGH-244A chip. I 
 downloaded and unzipped the .gz of the 
 HG-CGH-244A,TCGA,HB20080512,unitNames.txt and 
 HG-CGH-244A,TCGA,HB20080512.ugp and put them in 
 H:\Aroma_Analysis\annotationData\chipTypes\HG-CGH-244A folder. Then I tried 
 to run the same code on the vignette and got the error right away (please 
 see end of this email). Did I do something wrong?

 I have one more question regarding Creating data files containing log2 CN 
 ratios with HG-CGH-244A chip. The data I have are level 2 files from TCGA. 
 There is one txt file for each sample (not the original .asb file) and its 
 format is like:


 Hybridization REF MSK_1_251469322729_S01_CGH-v4_91

 Composite Element REF normalizedLog2Ratio

 A_14_P112718 0.135431541355747

 A_16_P15000916 0.441719513563848

 A_16_P15001074 0.227252175271962

 A_16_P0012 0.231158251618718

 A_16_P0014 -0.0623833233443793

 .

 ..

 My first question is, does this kind data file work?

 My second question is, do I need to create a folder rawCnData as mentioned 
 in the vignette (Pathname: 
 rawCnData/MyDataSet,tagA,tagB/HG-CGH-244A/SampleA,tagA,tagB,log2ratio,total.asb)?
   I also have the rawData folder which holds affy snp6 and expression data.



 Thanks a lot for the help!



 Ying

  library(aroma.core)
  chipType - HG-CGH-244A
  unf - TextUnitNamesFile$byChipType(chipType)
 Error in method(static, ...) :
 [2012-05-15 12:12:26] Exception: Failed to create TextUnitNamesFile object. 
 Could to locate an annotation data file for chip type 'HG-CGH-244A' (without 
 requiring any tags) and with filename extension 'names' (this may not be the 
 correct extension as it was guessed from the class name 'TextUnitNamesFile').

   at #02. method(static, ...)
   - method() is in environment 'aroma.core'
   at #01. TextUnitNamesFile$byChipType(chipType)
   - TextUnitNamesFile$byChipType() is local of the calling function
  sessionInfo()
 R version 2.15.0 (2012-03-30)
 Platform: x86_64-pc-mingw32/x64 (64-bit)
 locale:
 [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United 
 States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C
 [5] LC_TIME=English_United States.1252
 attached base 

Re: [aroma.affymetrix] Paired CBS

[Pierre Neuvial]

Hi Michelle,

Yes: just replace

plotTracks(fit);

by

plotTracks(fit, chromosome=2);

Best,

Pierre

On Mon, May 7, 2012 at 11:48 PM, Michelle suyi...@gmail.com wrote:
 Hi Henrik,

 On this page http://aroma-project.org/vignettes/PairedPSCBS-lowlevel you
 showed how to make whole genome plots of  TCN, the
 decrease-of-heterozygosity (DH), and the minor-major CN estimates. Is there
 a way to make such plots for individual chromosomes?

 Thanks,
 Michelle



 On Fri, Feb 17, 2012 at 6:04 PM, Henrik Bengtsson h...@biostat.ucsf.edu
 wrote:

 Hi,

 On Fri, Feb 17, 2012 at 1:44 PM, Michelle suyi...@gmail.com wrote:
  Hi Henrik,
 
  I ran the PSCBS package on some Affy SNP 6.0 arrays. In the output I
  found
  that several files contain a few lines of negative tcnMean values,
  while
  the rest are all positive. My question is - the total copy number is
  supposed to be positive, right? Are these negative values caused by some
  error in the computation? If so, how to adjust them?

 yes, *true*/*biological* CNs cannot be negative.  However,
 *observed*/*estimated* ones may very well end up being *slightly*
 negative, due to noise in data.  So, it is neither a bug nor something
 wrong with PSCBS.

 There is nothing in Paired PSCBS that enforces the CNs to be strictly
 non-negative (= 0), neither does it restrict the CN estimates to be
 integers (0, 1, 2, 3, ...), because there may be normal cell
 contamination or tumor clonality.  However, you can imagine that there
 are downstream methods that takes the PSCBS estimates and make such
 decisions, but that is not part of PSCBS itself.

 You can always manual adjust negative estimates to be zero, if you
 really need them not to be negative, but I still haven't had to do it.

 /Henrik

 
  Thanks,
  Michelle
 
  --
  When reporting problems on aroma.affymetrix, make sure 1) to run the
  latest
  version of the package, 2) to report the output of sessionInfo() and
  traceback(), and 3) to post a complete code example.
 
 
  You received this message because you are subscribed to the Google
  Groups
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  http://www.aroma-project.org/forum/

 --
 When reporting problems on aroma.affymetrix, make sure 1) to run the
 latest version of the package, 2) to report the output of sessionInfo() and
 traceback(), and 3) to post a complete code example.


 You received this message because you are subscribed to the Google Groups
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 To post to this group, send email to aroma-affymetrix@googlegroups.com
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 --
 When reporting problems on aroma.affymetrix, make sure 1) to run the latest
 version of the package, 2) to report the output of sessionInfo() and
 traceback(), and 3) to post a complete code example.


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version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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Re: [aroma.affymetrix] Error in Paired PSCBS with CytoScanHD

[Pierre Neuvial]

Hi,

On Wed, Apr 18, 2012 at 3:05 PM, Sathish Periyasamy 
sathish.periyas...@gmail.com wrote:

 I am getting the following error segs - getSegments(fit); The error
 output is as follows:

 Please assist me in solving the following error.

 regards

chromosome tcnId dhId tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs 
 tcnNbrOfHets
1 25 11 1598  16148   26   1.955   26  
   1
  dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean
11598 16148   1 0.3252 0.6596  1.295 chromosome tcnId dhId 
 tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets
1 25 11 1598  16148   26   1.955   26  
   1
  dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean
11598 16148   1 0.3252 0.6596  1.295 chromosome tcnId dhId 
 tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets
1 25 11 1598  16148   26   1.955   26  
   1
  dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean
11598 16148   1 0.3252 0.6596  1.295 chromosome tcnId dhId 
 tcnStart tcnEnd tcnNbrOfLoci tcnMean tcnNbrOfSNPs tcnNbrOfHets
1 25 11 1598  16148   26   1.955   26  
   1
  dhStart dhEnd dhNbrOfLoci dhMean c1Mean c2Mean
11598 16148   1 0.3252 0.6596  1.29520120418 15:49:56|  
 Chromosome #25 ('Chr25') of 25...done20120418 15:49:56|  Merging 
 (independently) segmented chromosome...Error: cannot allocate vector of size 
 17.3 Mb


The first error is actually here (just above).

17.3 Mb is really not much, and should not be a problem.  Maybe you have
large objects in your R session.  Can you try again from a fresh R session ?
Another possibility is that you have other programs than R taking all your
RAM.

More below.



 In addition: There were 50 or more warnings (use warnings() to see the first 
 50)20120418 15:50:43|  Merging (independently) segmented 
 chromosome...done20120418 15:50:43| Segmenting multiple 
 chromosomes...done20120418 15:50:43|Segmenting paired tumor-normal signals 
 using Paired PSCBS...done  segs - getSegments(fit);Error in 
 UseMethod(getSegments) :
   no applicable method for 'getSegments' applied to an object of class 
 function


Your 'fit' object was not created because of the above error, hence this
second error ('fit' is also a function in your R environment).

Cheers,

Pierre

 #segs - getSegments(fit); print(segs);Error in print(segs) : object 'segs' 
 not found #help(segmentByPairedPSCBS, package=PSCBS);  pairName - 
 paste(pair, collapse=vs); chrTag - sprintf(Chr%s, 
 seqToHumanReadable(getChromosomes(fit)));Error in UseMethod(getChromosomes) 
 :
   no applicable method for 'getChromosomes' applied to an object of class 
 function  toPNG(pairName, tags=c(chrTag, PairedPSCBS), width=840, 
 aspectRatio=0.6, {+   plotTracks(fit);+ });Error in paste(c(name, tags), 
 collapse = ,) : object 'chrTag' not found

 

 --
 When reporting problems on aroma.affymetrix, make sure 1) to run the
 latest version of the package, 2) to report the output of sessionInfo() and
 traceback(), and 3) to post a complete code example.


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Re: [aroma.affymetrix] Re: ACNE getGenomeInformation(cdf) failed

[Pierre Neuvial]

Hi,



On Thu, Apr 5, 2012 at 10:17 AM, Frederic Foucault
frederic.fouca...@gmail.com wrote:
 Hello,

 I follow the setup of the vignette but failed again

 setwd(c:/Users/foucault/Bioinformatic/acne/Test/)
 library(aroma.affymetrix);
 library(ACNE);
 verbose - Arguments$getVerbose(-10, timestamp=TRUE);

 dataSet - GSE14996,testSet;

 chipType - GenomeWideSNP_6;
 cdf - AffymetrixCdfFile$byChipType(chipType, tags=Full);
 print(cdf);
 AffymetrixCdfFile:
 Path: annotationData/chipTypes/GenomeWideSNP_6
 Filename: GenomeWideSNP_6,Full.cdf
 Filesize: 470.44MB
 Chip type: GenomeWideSNP_6,Full
 RAM: 0.00MB
 File format: v4 (binary; XDA)
 Dimension: 2572x2680
 Number of cells: 6892960
 Number of units: 1881415
 Cells per unit: 3.66
 Number of QC units: 4

 gi - getGenomeInformation(cdf);
 Error in getGenomeInformation.AffymetrixCdfFile(cdf) :
 [2012-04-05 10:12:33] Exception: Failed to retrieve genome information for
 this chip type: GenomeWideSNP_6


   at #02. getGenomeInformation.AffymetrixCdfFile(cdf)
   - getGenomeInformation.AffymetrixCdfFile() is in environment
 'aroma.affymetrix'

   at #01. getGenomeInformation(cdf)
   - getGenomeInformation() is in environment 'aroma.affymetrix'

 Thank you for your help,
 Frederic



Did you place all the annotation files in the
annotationData/chipTypes/GenomeWideSNP_6 folder ?
It looks that this one is missing :

GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp

Do these file appear in the output of

path - getPath(cdf)
list.files(path)

If not, then add them and retry.
If yes then I'm missing something.

Cheers,

Pierre

Pierre



 Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit :

 Hello,

 I want to get allele specific copy number from SNP6 CL files
 I´m following the vignette for ACNE.
 I installed the annotation data  in \test\annotationData\chipTypes
 \GenomeWideSNP6.0

 GenomeWideSNP_6,Full,HB20080710.acs
 GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl
 GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp
 GenomeWideSNP_6,Full.cdf

 GenomeWideSNP_6,Full.cdf is from Affymetrix while the three others are
 from aroma

 here is the error :
 gi - getGenomeInformation(cdf);
 Error in getGenomeInformation.AffymetrixCdfFile(cdf) :
 [2012-04-04 16:48:48] Exception: Failed to retrieve genome information
 for this chip type: GenomeWideSNP_6

   at #02. getGenomeInformation.AffymetrixCdfFile(cdf)
           - getGenomeInformation.AffymetrixCdfFile() is in environment
 'aroma.affymetrix'

   at #01. getGenomeInformation(cdf)
           - getGenomeInformation() is in environment
 'aroma.affymetrix'


 Thank you for your help
 Frederic


 Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit :

 Hello,

 I want to get allele specific copy number from SNP6 CL files
 I´m following the vignette for ACNE.
 I installed the annotation data  in \test\annotationData\chipTypes
 \GenomeWideSNP6.0

 GenomeWideSNP_6,Full,HB20080710.acs
 GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl
 GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp
 GenomeWideSNP_6,Full.cdf

 GenomeWideSNP_6,Full.cdf is from Affymetrix while the three others are
 from aroma

 here is the error :
 gi - getGenomeInformation(cdf);
 Error in getGenomeInformation.AffymetrixCdfFile(cdf) :
 [2012-04-04 16:48:48] Exception: Failed to retrieve genome information
 for this chip type: GenomeWideSNP_6

   at #02. getGenomeInformation.AffymetrixCdfFile(cdf)
           - getGenomeInformation.AffymetrixCdfFile() is in environment
 'aroma.affymetrix'

   at #01. getGenomeInformation(cdf)
           - getGenomeInformation() is in environment
 'aroma.affymetrix'


 Thank you for your help
 Frederic


 Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit :

 Hello,

 I want to get allele specific copy number from SNP6 CL files
 I´m following the vignette for ACNE.
 I installed the annotation data  in \test\annotationData\chipTypes
 \GenomeWideSNP6.0

 GenomeWideSNP_6,Full,HB20080710.acs
 GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl
 GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp
 GenomeWideSNP_6,Full.cdf

 GenomeWideSNP_6,Full.cdf is from Affymetrix while the three others are
 from aroma

 here is the error :
 gi - getGenomeInformation(cdf);
 Error in getGenomeInformation.AffymetrixCdfFile(cdf) :
 [2012-04-04 16:48:48] Exception: Failed to retrieve genome information
 for this chip type: GenomeWideSNP_6

   at #02. getGenomeInformation.AffymetrixCdfFile(cdf)
           - getGenomeInformation.AffymetrixCdfFile() is in environment
 'aroma.affymetrix'

   at #01. getGenomeInformation(cdf)
           - getGenomeInformation() is in environment
 'aroma.affymetrix'


 Thank you for your help
 Frederic


 Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit :

 Hello,

 I want to get allele specific copy number from SNP6 CL files
 I´m following the vignette for ACNE.
 I installed the annotation data  in \test\annotationData\chipTypes
 \GenomeWideSNP6.0

 

Re: [aroma.affymetrix] core dump error after upgrading R

[Pierre Neuvial]

What is your sessionInfo() ?

Perhaps you need to upgrade aroma.affymetrix instead, although I don't
see why you would get this core dump.

Pierre

On Mon, Nov 7, 2011 at 6:20 PM, Peter Kang h.peter.k...@gmail.com wrote:
 I just upgraded to 2.14.0 (Mac OSX), and I'm getting a 'core dumped'
 error when trying to access the cdf file.

 cdf - AffymetrixCdfFile$byChipType(Mapping250K_Nsp)
 print(cdf)
 zsh: abort (core dumped)  R

 Do I need to downgrade R?

 Thank you.

 --
 When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
 version of the package, 2) to report the output of sessionInfo() and 
 traceback(), and 3) to post a complete code example.


 You received this message because you are subscribed to the Google Groups 
 aroma.affymetrix group with website http://www.aroma-project.org/.
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-- 
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version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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Re: [aroma.affymetrix] Problem with doCRMAv2

[Pierre Neuvial]

Hi Ivan,

On Tue, Oct 25, 2011 at 1:35 AM, Ivan Smirnov vanya...@gmail.com wrote:
 Hi Henrik,

 I am trying to run the script:

 options(echo = FALSE,digits=4)
 library(aroma.affymetrix)
 verbose - Verbose(threshold=-8, timestamp=TRUE);
 dataSet=Gupta_CC
 chipType - GenomeWideSNP_6
 cdf - AffymetrixCdfFile$byChipType(chipType, tags=Full);
 print(cdf)
 dsList - doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE, verbose=verbose);
 dsC - dsList$total;
 print(dsC);


 and it is crushing with:

 20111024 16:05:12|   Normalizing set for PCR fragment-length effects...
 20111024 16:05:12|    Identifying SNP and CN units...
     types
          1      2      5
        621 934968 945826
 20111024 16:05:13|     subsetToUpdate:
      int [1:1880794] 622 623 624 625 626 627 628 629 630 631 ...
 20111024 16:05:13|    Identifying SNP and CN units...done
 20111024 16:05:13|    Retrieving SNP information annotations...
 20111024 16:05:13|     Defining DChipSnpInformation from chip type...
 20111024 16:05:13|      Chip type: GenomeWideSNP_6
 20111024 16:05:13|      Version:
 20111024 16:05:13|      Located pathname:
 20111024 16:05:13|     Defining DChipSnpInformation from chip type...done

Do you have UGP and UFL annotation files in your
annotationData/chipTypes/GenomeWideSNP_6 ?  From the above error it
looks like
instead you have (very) old SNP annotation files, which are not used
anymore within the Aroma Project, cf

http://www.mail-archive.com/aroma-affymetrix@googlegroups.com/msg01456.html

If you don't have UGP and UFL annotation files, please download them from

http://www.aroma-project.org/chipTypes/GenomeWideSNP_6

Hope this helps,

Pierre.

 Error in list(`doCRMAv2(dataSet, cdf = cdf, combineAlleles = FALSE,
 verbose = verbose)` = environment,  :

 [2011-10-24 16:05:13] Exception: Failed to retrieve SNP information
 for this chip type: GenomeWideSNP_6
  at throw(Exception(...))
  at throw.default(Failed to retrieve SNP information for this chip type: , 
 ch
  at throw(Failed to retrieve SNP information for this chip type: , chipType)
  at getSnpInformation.AffymetrixCdfFile(cdf)
  at getSnpInformation(cdf)
  at process.FragmentLengthNormalization(fln, verbose = verbose)
  at process(fln, verbose = verbose)
  at doCRMAv2.AffymetrixCelSet(csR, ..., verbose = verbose)
  at doCRMAv2(csR, ..., verbose = verbose)
  at doCRMAv2.character(dataSet, cdf = cdf, combineAlleles = FALSE, verbose = 
 ve
  at doCRMAv2(dataSet, cdf = cdf, combineAlleles = FALSE, verbose = verbose)
 Calls: doCRMAv2 ... getSnpInformation.AffymetrixCdfFile - throw -
 throw.default - throw - throw.Exception
 20111024 16:05:13|    Retrieving SNP information annotations...done
 20111024 16:05:13|   Normalizing set for PCR fragment-length effects...done
 Execution halted


 So, it seems to have problem getting info from CDF file. But
 print(cdf) looks normal:

 AffymetrixCdfFile:
 Path: annotationData/chipTypes/GenomeWideSNP_6
 Filename: GenomeWideSNP_6,Full.cdf
 Filesize: 470.44MB
 Chip type: GenomeWideSNP_6,Full
 RAM: 0.00MB
 File format: v4 (binary; XDA)
 Dimension: 2572x2680
 Number of cells: 6892960
 Number of units: 1881415
 Cells per unit: 3.66
 Number of QC units: 4

 and the check sum is identical to one posted on the web:
 3fbe0f6e7c8a346105238a3f3d10d4ec

 All my software is up to date. Any clues?

 Thanks
 Ivan

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Re: [aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file

[Pierre Neuvial]

Hi,

Have you tried using extractAffyBatch, which is documented here:
http://aroma-project.org/howtos/extractAffyBatch ?
As far as I understand you will need the Bioconductor annotation
package corresponding to your chip type to be installed, ie

 source(http://www.bioconductor.org/biocLite.R;)
 biocLite(hgu133plus2cdf)

This is discussed in this thread:
http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/40e3950e52d73c1f/772e387a3163db56

Pierre

On Tue, Aug 9, 2011 at 4:34 AM, hsingjun cheung
hsingjun.ch...@gmail.com wrote:
 Hi Pierre:

 Thanks. These functions work now. Do you know how to extract the raw
 intensity for each probe ?

 On Aug 8, 5:48 pm, Pierre Neuvial pie...@stat.berkeley.edu wrote:
 Hi,

 The 'annotationData' directory should be directly in your working
 directory, as explained in the page Setup: Location of annotation
 data files:http://aroma-project.org/node/66

 In your case, you need to change the current directory to ~/experiment/ by

 setwd(~/experiment/)

 (or by starting your R session from this directory).  Then your command

 csR - AffymetrixCelSet$byName(KN01M013,chipType=HG-U133_Plus_2)

 should work.

 Best,

 Pierre

 On Mon, Aug 8, 2011 at 5:29 PM, hsingjun cheung







 hsingjun.ch...@gmail.com wrote:
  Hello:

  I searched the group but got no results ... So I want to know, how to
  extract the raw probe intensity from .CEL file?

  The file structure on my computer is like:

  ~/experiemnt/
              annotationData/
                          chipTypes/
                                 HG-U133_Plus_2/
                                            HG-U133_Plus_2.cdf
  ~/experiment/
                rawData/
                        KN01M013/
                                HG-U133_Plus_2/
                                                     KN01M013.CEL

  The .cdf file is downloaded 
  fromhttp://www.aroma-project.org/chipTypes/HG-U133_Plus_2

  When I run R under ~ directory:
  library(aroma.affymetrix)
   csR - AffymetrixCelSet$byName(KN01M013,chipType=HG-U133_Plus_2)

  I got error msg:

  Error in list(`AffymetrixCelSet$byName(KN01M013, chipType = HG-
  U133_Plus_2)` = environment,  :

  [2011-08-08 11:24:05] Exception: Could not locate a file for this chip
  type: HG-U133_Plus_2
   at throw(Exception(...))
   at throw.default(Could not locate a file for this chip type: ,
  paste(c(chipT
   at throw(Could not locate a file for this chip type: ,
  paste(c(chipType, tag
   at method(static, ...)
   at AffymetrixCdfFile$byChipType(chipType)
   at method(static, ...)
   at AffymetrixCelSet$byName(KN01M013, chipType = HG-U133_Plus_2)

  Could anyone help me figure how this error happened ? And how to do
  it  ( extract raw probe intensity ) in a right way ? Thanks

  --
  When reporting problems on aroma.affymetrix, make sure 1) to run the 
  latest version of the package, 2) to report the output of sessionInfo() 
  and traceback(), and 3) to post a complete code example.

  You received this message because you are subscribed to the Google Groups 
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 --
 When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
 version of the package, 2) to report the output of sessionInfo() and 
 traceback(), and 3) to post a complete code example.


 You received this message because you are subscribed to the Google Groups 
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Re: [aroma.affymetrix] How to extract raw probe intensity from .CEL file

[Pierre Neuvial]

Hi,

The 'annotationData' directory should be directly in your working
directory, as explained in the page Setup: Location of annotation
data files:
http://aroma-project.org/node/66

In your case, you need to change the current directory to ~/experiment/ by

setwd(~/experiment/)

(or by starting your R session from this directory).  Then your command

csR - AffymetrixCelSet$byName(KN01M013,chipType=HG-U133_Plus_2)

should work.

Best,

Pierre

On Mon, Aug 8, 2011 at 5:29 PM, hsingjun cheung
hsingjun.ch...@gmail.com wrote:
 Hello:

 I searched the group but got no results ... So I want to know, how to
 extract the raw probe intensity from .CEL file?

 The file structure on my computer is like:

 ~/experiemnt/
             annotationData/
                         chipTypes/
                                HG-U133_Plus_2/
                                           HG-U133_Plus_2.cdf
 ~/experiment/
               rawData/
                       KN01M013/
                               HG-U133_Plus_2/
                                                    KN01M013.CEL

 The .cdf file is downloaded from 
 http://www.aroma-project.org/chipTypes/HG-U133_Plus_2

 When I run R under ~ directory:
 library(aroma.affymetrix)
  csR - AffymetrixCelSet$byName(KN01M013,chipType=HG-U133_Plus_2)

 I got error msg:

 Error in list(`AffymetrixCelSet$byName(KN01M013, chipType = HG-
 U133_Plus_2)` = environment,  :

 [2011-08-08 11:24:05] Exception: Could not locate a file for this chip
 type: HG-U133_Plus_2
  at throw(Exception(...))
  at throw.default(Could not locate a file for this chip type: ,
 paste(c(chipT
  at throw(Could not locate a file for this chip type: ,
 paste(c(chipType, tag
  at method(static, ...)
  at AffymetrixCdfFile$byChipType(chipType)
  at method(static, ...)
  at AffymetrixCelSet$byName(KN01M013, chipType = HG-U133_Plus_2)



 Could anyone help me figure how this error happened ? And how to do
 it  ( extract raw probe intensity ) in a right way ? Thanks


 --
 When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
 version of the package, 2) to report the output of sessionInfo() and 
 traceback(), and 3) to post a complete code example.


 You received this message because you are subscribed to the Google Groups 
 aroma.affymetrix group with website http://www.aroma-project.org/.
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version of the package, 2) to report the output of sessionInfo() and 
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Re: [aroma.affymetrix] aroma.affymetrix can't read cdf file

[Pierre Neuvial]

Hi Yaping,

The cdf file should not be in the working directory, but in a
chip-type-specific subdirectory of the 'annotationData' directory, as
explained in the page Setup: Location of annotation data files:
http://aroma-project.org/node/66

Please see this page for further info.  In your example, the cdf file
should be in

  annotationData/chipTypes/Mapping250K_Nsp

Best,

Pierre

On Thu, Aug 4, 2011 at 11:20 PM, Yaping Feng yapi...@gmail.com wrote:
 hi,
 I just installed aroma.affymetrix in my mac computer (Mac OS X 10.6.7). The
 R version is 2.13.1.
 I want to read this cdf file Mapping250K_Nsp.cdf:

 cdf - AffymetrixCdfFile$byChipType(Mapping250K_Nsp)

 Error in list(`AffymetrixCdfFile$byChipType(Mapping250K_Nsp)` =
 environment,  :

 [2011-08-04 16:01:17] Exception: Could not locate a file for this chip type:
 Mapping250K_Nsp
  at throw(Exception(...))
  at throw.default(Could not locate a file for this chip type: ,
 paste(c(chipType, tags), collapse = ,))
  at throw(Could not locate a file for this chip type: , paste(c(chipType,
 tags), collapse = ,))
  at method(static, ...)
  at AffymetrixCdfFile$byChipType(Mapping250K_Nsp)


 The cdf file is in the current directory. Can anybody tell me how to fix it!
 Thanks,
 Yaping

 --
 When reporting problems on aroma.affymetrix, make sure 1) to run the latest
 version of the package, 2) to report the output of sessionInfo() and
 traceback(), and 3) to post a complete code example.


 You received this message because you are subscribed to the Google Groups
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version of the package, 2) to report the output of sessionInfo() and 
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Re: [aroma.affymetrix] Aroma Affymetrix shell variable path?

[Pierre Neuvial]

Hi Fong,

The standard way to do this within the Aroma framework is to use
*links* to the directories you need.  The best way to do this depends
on your OS, but in general this can be done within R using the
function 'createLink' (from R.utils), e.g.:

 createLink(target=~/Data/annotationData)
 createLink(target=~/Data/rawData)

will create in the working directory a link to ~/Data/annotationData
called annotationData, and a link to ~/Data/rawData called
rawData.

In general I think that it is very sound to separate the actual
location of the data from the location of your scripts, and that's
exactly what you can do with links.

Note that if you'd like the results of your analyses to be written in
your usual data directory (~/Data in the above example) instead of
your current working directory, then you will also have to do
something like

 createLink(target=~/Data/probeData)
 createLink(target=~/Data/plmData)

Hope this helps,

Pierre

On Mon, Mar 14, 2011 at 7:09 PM, Fong fongchunc...@gmail.com wrote:
 Hi,

 Is there a way to use aroma affymetrix code without having to be in
 the aroma affymetrix directory?  When I am outside of the aroma
 affymetrix directory and I try to enter the command:

 cdf - AffymetrixCdfFile$byChipType('HG-U133_Plus_2', tags='ense')
 Error in list(`AffymetrixCdfFile$byChipType(HG-U133_Plus_2, tags =
 ense)` = environment,  :

 [2011-03-14 10:56:12] Exception: Could not locate a file for this chip
 type: HG-U133_Plus_2,ense
  at throw(Exception(...))
  at throw.default(Could not locate a file for this chip type: ,
 paste(c(chipT
  at throw(Could not locate a file for this chip type: ,
 paste(c(chipType, tag
  at method(static, ...)
  at AffymetrixCdfFile$byChipType(HG-U133_Plus_2, tags = ense)


 All this code is in a R script and the easy solution would be to set
 the directory to that be the aroma affymetrix directory using
 setwd().  But I was wondering if there was some aroma affymetrix shell
 variable I could set so that it knows where to look for the aroma
 affymetrix files without having to explicitly set the directory.  I
 haven't been able to find any references to this in the forums.

 Thanks,

 Fong

 --
 When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
 version of the package, 2) to report the output of sessionInfo() and 
 traceback(), and 3) to post a complete code example.


 You received this message because you are subscribed to the Google Groups 
 aroma.affymetrix group with website http://www.aroma-project.org/.
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version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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Re: [aroma.affymetrix] fracB and BAF values

[Pierre Neuvial]

Hi Allab,

'fracB' in the Aroma world has the same meaning as 'BAF' in the
Illumina BeadStudio world, that is, as you say, the fraction of signal
coming from the B allele at a given SNP:  yB/(yA+yB).  So the short
answer is that there is no conversion needed from 'fracB' to 'BAF'.

[Side note: we decided to call it 'fracB' instead of BAF because we
believe that the term 'frequency' is misleading as it suggests a
calculation across a population of samples.]

More details: In BeadStudio the BAF signals are truncated at 0 and 1,
which is why you only observe values in this range.  On the other
hand, aroma.affymetrix implements (AS)-CRMAv2, in which signals are
*not* truncated, mainly because such a truncation results in a loss of
information.  In particular, truncation introduces non-linearities in
the signals, which is not always (and IMHO, generally not) a good
idea.  If you want values between 0 and 1, you can still truncate them
afterwards.

Even more details: the main reason why there are values out of the
range in the first place is that raw intensity values are corrected
for offset and allelic crosstalk (see the CRMA v1 and CRMA v2 papers
in http://aroma-project.org/publications).  Note that a similar type
of correction is performed by BeadStudio, but truncation hides the
values outside of [0,1].

Does this answer your question ?

Best,

Pierre

On Mon, Dec 20, 2010 at 5:51 PM, allab asphod...@googlemail.com wrote:
 Dear aroma users/authors,
 i am doing now Affy 6.0 SNP data analysis and my goal is to become BAF
 values (B-allele frequency) as they were output from Illumina
 software.
 BAF is a normalized metric which reflects the proportion of B-alleles
 in each SNP, e.g. 0 for AA SNP, 0.5 for an AB SNP and 1 for BB.
 I have generated fracB values with aroma package and see now that
 there are also negative values for fracB, but as i understand it
 correctly BAF values should be in the range between 0 and 1.
 The question is, how can i convert fracB values into BAF values.
 Thank you in Advance.

 --
 When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
 version of the package, 2) to report the output of sessionInfo() and 
 traceback(), and 3) to post a complete code example.


 You received this message because you are subscribed to the Google Groups 
 aroma.affymetrix group with website http://www.aroma-project.org/.
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-- 
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version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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Re: [aroma.affymetrix] DNA segmentation result

[Pierre Neuvial]

Hi,

Sure, it will be quicker.

In this case, you only have to setup the CBS segmentation model, and
fit it.  For example:

## define the segmentation model
## (and its parameters)
seg - CbsModel(ds, min.width=5);

## perform the segmentation
## (possibly for a subset of arrays and chromosomes)
fit(seg, array=2, chromosome=5, verbose=TRUE);

There are other examples on the aroma project website, e.g.
http://aroma-project.org/vignettes/pairedTotalCopyNumberAnalysis

Best,

Pierre

On Mon, Nov 29, 2010 at 7:33 PM, Yan Jiao y.j...@ucl.ac.uk wrote:
 Hi,

 Sorry to bother you again

 If I don't need the chromosome Explorer as result, I just need that excel 
 file with copy number in (regions.xls, in CBS folder), how should I set the 
 parameter, I guess it will speed up the procedure as well, right?

 Many thanks

 yan

 -Original Message-
 From: aroma-affymetrix@googlegroups.com 
 [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
 Sent: 28 November 2010 22:57
 To: aroma-affymetrix
 Subject: Re: [aroma.affymetrix] DNAcopy parameter

 On Sun, Nov 28, 2010 at 6:01 AM, Pierre Neuvial
 pie...@stat.berkeley.edu wrote:
 Hi,

 The parameters used are the default parameters of the 'segment'
 function of the DNAcopy package.  If you search for 'DNAcopy
 parameters' on the Search forum box at http://aroma-project.org, you
 will find this recent thread which gives an example of how these
 parameters can be changed:

 http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/aa9db6ac7835d828/b6ab6b1c9786d9ff

 Note that I just posted a follow up on that thread clarified that it
 is now possible to specify optional arguments specific to
 DNAcopy::segment() as:

 seg - CbsModel(ds, min.width=5);

 In order to find out which they are and what they do, see the specific
 segmentation method, i.e. help(segment, package=DNAcopy).

 /Henrik


 Hope this helps.

 Pierre

 On Wed, Nov 24, 2010 at 7:31 PM, Yan Jiao y.j...@ucl.ac.uk wrote:
 Thanks Henrik,
 I will update my R and aroma package,
 Another question is what kind of parameters of aroma use for copy number
 segmentation, if using DNAcopy as the algorithm?

 Many thanks

 yan

 -Original Message-
 From: aroma-affymetrix@googlegroups.com
 [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
 Sent: 24 November 2010 17:06
 To: aroma-affymetrix
 Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error

 Ok, after seing your sessionInfo();

 You need to update to R v2.12.0, especially since you're on Windows
 64-bit.  Lots of work have been done by R core people to support
 Windows 64-bit on R v2.12.0 and beyond.  There is no shortcut to this.

 Update aroma.affymetrix to v1.8.0, cf. http://aroma-project.org/install

 Also, the Cairo package is not available for the 64-bit version of R
 on Windows.  If you try install.packages(Cairo) on your Windows
 machine, CRAN should report that package is not available.   Either
 you have installed it by other means or it incorrectly installed on R
 v2.11.0.

 /Henrik


 On Wed, Nov 24, 2010 at 8:58 AM, Yan Jiao y.j...@ucl.ac.uk wrote:
 Hi Henrik,

 I did what you suggested:

 traceback()

 13: stop(gettextf(package '%s' is not installed for 'arch=%s',

     pkgname, r_arch), call. = FALSE, domain = NA)

 12: testRversion(pkgInfo, package, pkgpath)

 11: library(package, lib.loc = lib.loc, character.only = TRUE,
 logical.return = TRUE,

     warn.conflicts = warn.conflicts, keep.source = keep.source)

 10: base::require(...)

 9: require(Cairo)

 8: findPngDevice.default(transparent = FALSE)

 7: findPngDevice(transparent = FALSE)

 6: plot.CopyNumberSegmentationModel(model, path = path, imageFormat =
 png,

    plotband = plotband, arrays = arrays, ...)

 5: plot(model, path = path, imageFormat = png, plotband = plotband,

    arrays = arrays, ...)

 4: writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes =
 chromosomes,

    zooms = zooms, ..., verbose = less(verbose))

 3: writeGraphs(this, arrays = arrays, chromosomes = chromosomes,

    zooms = zooms, ..., verbose = less(verbose))

 2: process.ChromosomeExplorer(ce.all, verbose = TRUE)

 1: process(ce.all, verbose = TRUE)

 sessionInfo()

 R version 2.11.0 (2010-04-22)

 x86_64-pc-mingw32

 locale:

 [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
 Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
 LC_NUMERIC=C

 [5] LC_TIME=English_United Kingdom.1252

 attached base packages:

 [1] stats graphics  grDevices utils datasets  methods   base

 other attached packages:

  [1] RColorBrewer_1.0-2 DNAcopy_1.22.1 preprocessCore_1.10.0
 sfit_0.1.9     aroma.affymetrix_1.7.0 aroma.apd_0.1.7
 affxparser_1.20.0

  [8] R.huge_0.2.0   aroma.core_1.7.0   aroma.light_1.16.1
 matrixStats_0.2.2  R.rsp_0.4.0    R.cache_0.3.0
 R.filesets_0.9.0

 [15] digest_0.4.2   R.utils_1.5.3  R.oo_1.7.4

Re: [aroma.affymetrix] subselect samples for segmentation

[Pierre Neuvial]

Hi Yan,

You're right: removing files manually from data folders generated by
aroma.* is not a good idea.  This is can be done directly within R
using the methods provided by the package.

In your case, I think you were doing :

cbs - CbsModel(ds);
ce - ChromosomeExplorer(cbs);
process(ce, chromosomes=c(1,8,17), verbose=TRUE);

To run the segmentation on the first two samples, you can do

process(ce, arrays=c(1,2), chromosomes=c(1,8,17), verbose=TRUE);

If you want to specify the *names* of samples to be segmented, you can use

idxs - indexOf(ce, sampleNames);
process(ce, arrays=idxs, chromosomes=c(1,8,17), verbose=TRUE);

where 'sampleNames' is a vector of sample names.

More generally, one can use the 'extract' method on any set of data files, e.g.

ds - doCRMAv1(Fockens_1, chipType=Mapping50K_Hind240, verbose=TRUE);
idxs - indexOf(ce, sampleNames);
dsSub - extract(ds, idxs);

Hope this helps.

Pierre



On Thu, Nov 25, 2010 at 3:35 PM, Yan Jiao y.j...@ucl.ac.uk wrote:
 Now it works after I update my R.
 Another question is can I pass the sample names as a parameter to sub select 
 the samples for segmentation? instead of removing the unwanted ones from data 
 folder?

 Many thanks

 yan

 -Original Message-
 From: aroma-affymetrix@googlegroups.com 
 [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
 Sent: 24 November 2010 17:06
 To: aroma-affymetrix
 Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error

 Ok, after seing your sessionInfo();

 You need to update to R v2.12.0, especially since you're on Windows
 64-bit.  Lots of work have been done by R core people to support
 Windows 64-bit on R v2.12.0 and beyond.  There is no shortcut to this.

 Update aroma.affymetrix to v1.8.0, cf. http://aroma-project.org/install

 Also, the Cairo package is not available for the 64-bit version of R
 on Windows.  If you try install.packages(Cairo) on your Windows
 machine, CRAN should report that package is not available.   Either
 you have installed it by other means or it incorrectly installed on R
 v2.11.0.

 /Henrik


 On Wed, Nov 24, 2010 at 8:58 AM, Yan Jiao y.j...@ucl.ac.uk wrote:
 Hi Henrik,

 I did what you suggested:

 traceback()

 13: stop(gettextf(package '%s' is not installed for 'arch=%s',

     pkgname, r_arch), call. = FALSE, domain = NA)

 12: testRversion(pkgInfo, package, pkgpath)

 11: library(package, lib.loc = lib.loc, character.only = TRUE,
 logical.return = TRUE,

     warn.conflicts = warn.conflicts, keep.source = keep.source)

 10: base::require(...)

 9: require(Cairo)

 8: findPngDevice.default(transparent = FALSE)

 7: findPngDevice(transparent = FALSE)

 6: plot.CopyNumberSegmentationModel(model, path = path, imageFormat = png,

    plotband = plotband, arrays = arrays, ...)

 5: plot(model, path = path, imageFormat = png, plotband = plotband,

    arrays = arrays, ...)

 4: writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes =
 chromosomes,

    zooms = zooms, ..., verbose = less(verbose))

 3: writeGraphs(this, arrays = arrays, chromosomes = chromosomes,

    zooms = zooms, ..., verbose = less(verbose))

 2: process.ChromosomeExplorer(ce.all, verbose = TRUE)

 1: process(ce.all, verbose = TRUE)

 sessionInfo()

 R version 2.11.0 (2010-04-22)

 x86_64-pc-mingw32

 locale:

 [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
 Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
 LC_NUMERIC=C

 [5] LC_TIME=English_United Kingdom.1252

 attached base packages:

 [1] stats graphics  grDevices utils datasets  methods   base

 other attached packages:

  [1] RColorBrewer_1.0-2 DNAcopy_1.22.1 preprocessCore_1.10.0
 sfit_0.1.9     aroma.affymetrix_1.7.0 aroma.apd_0.1.7
 affxparser_1.20.0

  [8] R.huge_0.2.0   aroma.core_1.7.0   aroma.light_1.16.1
 matrixStats_0.2.2  R.rsp_0.4.0    R.cache_0.3.0
 R.filesets_0.9.0

 [15] digest_0.4.2   R.utils_1.5.3  R.oo_1.7.4
 R.methodsS3_1.2.1

 loaded via a namespace (and not attached):

 [1] tools_2.11.0



 process(ce,chromosomes=c(1,8,17), verbose=-10)

 Generating ChromosomeExplorer report...

  Setting up ChromosomeExplorer report files...

   Copying template files...

    Source path:
 C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/includes

    Destination path: reports/includes

   Copying template files...done

  Setting up ChromosomeExplorer report files...done

  Explorer output version: 3

  Compiling ChromosomeExplorer.onLoad.js.rsp...

   Source:
 C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp

   Output path: reports/Fockens_1/ACC,-XY,RMA,+300,A+B,FLN,-XY

   Scanning directories for available chip types...

    Detected chip types: Mapping50K_Hind240

   Scanning directories for available chip types...done

   Scanning image files for available zooms...

    Detected (or default) zooms: 1, 2, 4, 

Re: [aroma.affymetrix] DNAcopy parameter

[Pierre Neuvial]

Hi,

The parameters used are the default parameters of the 'segment'
function of the DNAcopy package.  If you search for 'DNAcopy
parameters' on the Search forum box at http://aroma-project.org, you
will find this recent thread which gives an example of how these
parameters can be changed:

http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/aa9db6ac7835d828/b6ab6b1c9786d9ff

Hope this helps.

Pierre

On Wed, Nov 24, 2010 at 7:31 PM, Yan Jiao y.j...@ucl.ac.uk wrote:
 Thanks Henrik,
 I will update my R and aroma package,
 Another question is what kind of parameters of aroma use for copy number 
 segmentation, if using DNAcopy as the algorithm?

 Many thanks

 yan

 -Original Message-
 From: aroma-affymetrix@googlegroups.com 
 [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
 Sent: 24 November 2010 17:06
 To: aroma-affymetrix
 Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error

 Ok, after seing your sessionInfo();

 You need to update to R v2.12.0, especially since you're on Windows
 64-bit.  Lots of work have been done by R core people to support
 Windows 64-bit on R v2.12.0 and beyond.  There is no shortcut to this.

 Update aroma.affymetrix to v1.8.0, cf. http://aroma-project.org/install

 Also, the Cairo package is not available for the 64-bit version of R
 on Windows.  If you try install.packages(Cairo) on your Windows
 machine, CRAN should report that package is not available.   Either
 you have installed it by other means or it incorrectly installed on R
 v2.11.0.

 /Henrik


 On Wed, Nov 24, 2010 at 8:58 AM, Yan Jiao y.j...@ucl.ac.uk wrote:
 Hi Henrik,

 I did what you suggested:

 traceback()

 13: stop(gettextf(package '%s' is not installed for 'arch=%s',

     pkgname, r_arch), call. = FALSE, domain = NA)

 12: testRversion(pkgInfo, package, pkgpath)

 11: library(package, lib.loc = lib.loc, character.only = TRUE,
 logical.return = TRUE,

     warn.conflicts = warn.conflicts, keep.source = keep.source)

 10: base::require(...)

 9: require(Cairo)

 8: findPngDevice.default(transparent = FALSE)

 7: findPngDevice(transparent = FALSE)

 6: plot.CopyNumberSegmentationModel(model, path = path, imageFormat = png,

    plotband = plotband, arrays = arrays, ...)

 5: plot(model, path = path, imageFormat = png, plotband = plotband,

    arrays = arrays, ...)

 4: writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes =
 chromosomes,

    zooms = zooms, ..., verbose = less(verbose))

 3: writeGraphs(this, arrays = arrays, chromosomes = chromosomes,

    zooms = zooms, ..., verbose = less(verbose))

 2: process.ChromosomeExplorer(ce.all, verbose = TRUE)

 1: process(ce.all, verbose = TRUE)

 sessionInfo()

 R version 2.11.0 (2010-04-22)

 x86_64-pc-mingw32

 locale:

 [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
 Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
 LC_NUMERIC=C

 [5] LC_TIME=English_United Kingdom.1252

 attached base packages:

 [1] stats graphics  grDevices utils datasets  methods   base

 other attached packages:

  [1] RColorBrewer_1.0-2 DNAcopy_1.22.1 preprocessCore_1.10.0
 sfit_0.1.9     aroma.affymetrix_1.7.0 aroma.apd_0.1.7
 affxparser_1.20.0

  [8] R.huge_0.2.0   aroma.core_1.7.0   aroma.light_1.16.1
 matrixStats_0.2.2  R.rsp_0.4.0    R.cache_0.3.0
 R.filesets_0.9.0

 [15] digest_0.4.2   R.utils_1.5.3  R.oo_1.7.4
 R.methodsS3_1.2.1

 loaded via a namespace (and not attached):

 [1] tools_2.11.0



 process(ce,chromosomes=c(1,8,17), verbose=-10)

 Generating ChromosomeExplorer report...

  Setting up ChromosomeExplorer report files...

   Copying template files...

    Source path:
 C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/includes

    Destination path: reports/includes

   Copying template files...done

  Setting up ChromosomeExplorer report files...done

  Explorer output version: 3

  Compiling ChromosomeExplorer.onLoad.js.rsp...

   Source:
 C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp

   Output path: reports/Fockens_1/ACC,-XY,RMA,+300,A+B,FLN,-XY

   Scanning directories for available chip types...

    Detected chip types: Mapping50K_Hind240

   Scanning directories for available chip types...done

   Scanning image files for available zooms...

    Detected (or default) zooms: 1, 2, 4, 8, 16, 32, 64

   Scanning image files for available zooms...done

   Scanning directory for subdirectories...

    Detected (or default) sets: cbs

   Scanning directory for subdirectories...done

   Compiling RSP...

    member data.class dimension objectSize

    1    chipTypes  character 1    120

    2    chrLayers  character 0 40

    3 sampleLabels  character 3    240

    4 sampleLayers  character 0 40

    5  samples  character 3   

Re: [aroma.affymetrix] Copy number segmentation result

[Pierre Neuvial]

Hi,

On Wed, Nov 24, 2010 at 4:17 PM, Yan Jiao y.j...@ucl.ac.uk wrote:
 Hi Henrik,

 Another question about the result is : is there a way to map the copy number 
 to the gene ID automatically?

You mean retrieving a list of genes contained in each DNAcopy segment
?  No, this is not implemented in aroma.*
You can use (for example) the biomaRt package to do this.

 Also does aroma choose threshold for calling gain and loss?

No, aroma.* just calls the DNAcopy::segment function for you, and this
function just performs segmentation, and gives you the mean copy
number in each segment.  It does not call gains or losses.

Cheers,

Pierre


 Many thanks

 yan

 -Original Message-
 From: aroma-affymetrix@googlegroups.com 
 [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
 Sent: 24 November 2010 15:08
 To: aroma-affymetrix
 Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error

 Hi,

 great.  Contrary to error messages, warnings are alright to get.

 /H

 On Wed, Nov 24, 2010 at 2:51 AM, Yan Jiao y.j...@ucl.ac.uk wrote:
 Thank you Henrik,
 It works now, but I got some warning:

 process(ce, verbose=TRUE);
 Generating ChromosomeExplorer report...
 Loading required package: Cairo
 Generating ChromosomeExplorer report...done
 [1] TRUE
 Warning messages:
 1: In library(package, lib.loc = lib.loc, character.only = TRUE, 
 logical.return = TRUE,  :
  there is no package called 'Cairo'
 2: In method(static, ...) :
  Ghostscript not found. Searched directories: C:/gs, C:\Program Files/gs, 
 /gs, C:\Program Files\Common Files/gs

 Are those warning messages serious? Could I ignore them?


 Yan

 -Original Message-
 From: aroma-affymetrix@googlegroups.com 
 [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
 Sent: 23 November 2010 21:53
 To: aroma-affymetrix
 Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error

 Hi.

 On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao y.j...@ucl.ac.uk wrote:
 Hi Henrik,

 Sorry, the error is after
 cbs - CbsModel(ds);
 ce - ChromosomeExplorer(cbs);
 process(ce, verbose=TRUE);

 Ok, now the error message makes a bit more sense (it was my suspicion
 but I didn't want make guesses).



 Generating ChromosomeExplorer report...
 Loading required package: Cairo
 simpleError in inDL(x, as.logical(local), as.logical(now), ...): unable
 to load shared library
 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll':
  LoadLibrary failure:  The specified module could not be found.

 And there  is a pop out window saying: The program can't start because
 libgsl-0.dll I smissing from your computer. Try reinstalling the program
 to fix this program.

 I can reproduce this on 64-bit Windows 7 - you get the same error if
 you try library(GLAD).  It is because we utilize part of the GLAD
 package, if and only if it is *installed*, and otherwise we turn to
 backup solutions.  What happens here is that *GLAD is installed but
 doesn't load*, which causes the error so that backup solutions doesn't
 kick in.   In the next release I'll try to make sure the backup
 solutions will also work when there is an error load GLAD.  In
 meanwhile, you can do this:

 WORKAROUND:

 1. Uninstall the GLAD package (it doesn't work anyway):

 remove.packages(GLAD)
 Removing package(s) from 'C:\Users\hb\R\win-library\2.12'
 (as 'lib' is unspecified)

 library(GLAD)
 Error in library(GLAD) : there is no package called 'GLAD'

 That should do it.  Let me know if it works for you.

 TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL)
 is not installed on the system (hence the 'gsl' part of
 'libgsl-0.dll'). There is a hard-to-find note that you need GSL in
 order to use the GLAD package, cf.
 http://bioconductor.org/packages/release/bioc/html/GLAD.html.  There
 exist 32-bit binaries of GSL at
 http://gnuwin32.sourceforge.net/packages/gsl.htm.  Unfortunately, it
 does not work for the 64-bit version of R on Windows 64-bit.  It works
 if you do tricks an run the 32-bit version of R, but that is a rather
 inconvenient workaround.

 /Henrik



 Yan

 -Original Message-
 From: aroma-affymetrix@googlegroups.com
 [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
 Sent: 23 November 2010 18:50
 To: aroma-affymetrix
 Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error

 Hi.

 On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao y.j...@ucl.ac.uk wrote:


 Dear all,

 I'm trying to do DNA segmentation,

 This is what I'm doing:

 ds - doCRMAv1(Fockens_1, chipType=Mapping50K_Hind240,
 verbose=TRUE);

 ###this is done sucessfully

 # Segmentation

 cbs - CbsModel(ds);



 I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm
 trying
 to use DNAcopy for segmentation.

 Is it really the case that you get that error when you do:

 cbs - CbsModel(ds);

 or do you do anything else?  Is suspect you do something more.

 Also, after you got the error, could you cut'n'paste the verbose
 output including any error 

Re: [aroma.affymetrix] Problem with read CDF files

[Pierre Neuvial]

Hi Wero,

Dario is right, as explained in http://aroma-project.org/node/66.

Also, I would recommend not to manually add data in the installation
directories of R packages.  When you upgrade to a new version of R,
your data will still be stuck in the installation directory of the old
version.

Specificially, I would avoid (1) having your 'annotationData' (and all
the others aroma.* folders) in the directory where  aroma.affymetrix
is installed, and (2) using this installation directory as you working
directory.

See  http://aroma-project.org/node/79  for an example of setup.  Also,
remember that 'annotationData' in the working directory can be a
symbolic link to another directory on your file system.

Hope this helps,

Pierre

On Mon, Sep 27, 2010 at 5:05 PM, Dario Strbenac
d.strbe...@garvan.org.au wrote:
 Hello,

 You need to be in the directory above annotationData.

 - Dario.

  Original message 
Date: Mon, 27 Sep 2010 16:53:06 -0700 (PDT)
From: aroma-affymetrix@googlegroups.com (on behalf of Wero 
ivansk...@gmail.com)
Subject: [aroma.affymetrix] Problem with read CDF files
To: aroma.affymetrix aroma-affymetrix@googlegroups.com
Cc: ii...@inmegen.gob.mx

Hi, I have been trying to read the CDF files for the HuGene-1_0-st-v1
array with aroma.affymetrix and it has been very confuse for me.

I have the correct CDF files from the aroma page.

The CDF files are in the path: /Library/Frameworks/R.framework/
Versions/2.11/Resources/library/aroma.affymetrix/annotationData/
chipTypes/HuGene-1_0-st-v1.

My working directory is:  annotationData

but I still have this error:
#
 cdf - AffymetrixCdfFile$byChipType(chipType, tags=r3)
Error in list(`AffymetrixCdfFile$byChipType(chipType, tags = r3)` =
environment,  :

[2010-09-27 06:14:53] Exception: Could not locate a file for this chip
type: HuGene-1_0-st-v1,r3
  at throw(Exception(...))
  at throw.default(Could not locate a file for this chip type: , pa
  at throw(Could not locate a file for this chip type: , paste(c(ch
  at method(static, ...)
  at AffymetrixCdfFile$byChipType(chipType, tags = r3)
##

Also, if I look for the cdf path file in R, it returns NULL

pathname - 
annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.cdf

 cdf - AffymetrixCdfFile(pathname)
Error in list(`AffymetrixCdfFile(pathname)` = environment,
`extend(AromaChipTypeAnnotationFile(...), c(AffymetrixCdfFile, ` =
environment,  :

[2010-09-27 06:48:54] Exception: Pathname not found: annotationData/
chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.cdf (none of the parent
directories [annotationData/chipTypes/HuGene-1_0-st-v1/] exist;
current directory is '/Library/Frameworks/R.framework/Versions/2.11/
Resources/library/aroma.affymetrix/annotationData/chipTypes/HuGene-1_0-
st-v1')
  at throw(Exception(...))
  at throw.default(Pathname not found: , pathname, reason)
  at throw(Pathname not found: , pathname, reason)
  at method(static, ...)
  at Arguments$getReadablePathname(filename, path = path, mustExist =
  at GenericDataFile(...)
  at extend(GenericDataFile(...), AromaMicroarrayDataFile)
  at AromaMicroarrayDataFile(...)
  at extend(AromaMicroarrayDataFile(...), c(AffymetrixFile, uses(A
  at AffymetrixFile(...)
  at extend(AffymetrixFile(...), AromaChipTypeAnnotationFile)
  at AromaChipTypeAnnotationFile(...)
  at extend(AromaChipTypeAnnotationFile(...), c(AffymetrixCdfFile,
  at Affymetrix
In addition: Warning messages:
1: In is.na(parent) :
  is.na() applied to non-(list or vector) of type 'NULL'
2: In is.na(parent) :
  is.na() applied to non-(list or vector) of type 'NULL'
 pathname - getPathname(cdf)
 print(pathname)
[1] annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-
v1,r3.cdf

 pathname2 - AffymetrixCdfFile$findByChipType(HuGene-1_0-st-v1, tags=3)
 print(pathname2)
NULL

###
This is my sessionInfo()
R version 2.11.1 (2010-05-31)
i386-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods
[7] base

other attached packages:
 [1] oligoClasses_1.10.0    Biobase_2.8.0
 [3] aroma.affymetrix_1.7.0 aroma.apd_0.1.7
 [5] affxparser_1.20.0      R.huge_0.2.0
 [7] aroma.core_1.7.0       aroma.light_1.16.1
 [9] matrixStats_0.2.1      R.rsp_0.4.0
[11] R.cache_0.3.0          R.filesets_0.9.0
[13] digest_0.4.2           R.utils_1.5.2
[15] R.oo_1.7.4             oligo_1.12.2
[17] R.methodsS3_1.2.1

loaded via a namespace (and not attached):
[1] affyio_1.16.0         Biostrings_2.16.5     DBI_0.2-5
[4] IRanges_1.6.6         preprocessCore_1.10.0 splines_2.11.1
[7] tools_2.11.1


This is my traceback()
6: throw.Exception(Exception(...))
5: throw(Exception(...))
4: throw.default(msg)
3: throw(msg)
2: method(static, ...)
1: AffymetrixCdfFile$fromChipType(HuGene-1_0-st-v1, tags = r3)

###
I would appreciate any help, thanks!!!

Wero.

Re: [aroma.affymetrix] Analysis of GenomeWideSNP6.0 data

[Pierre Neuvial]

Hi,

On Tue, Aug 3, 2010 at 8:12 AM, Ajanthah Sangaralingam
a.sangaralin...@qmul.ac.uk wrote:
 Thank you for the reply. I  actually need to get the log2 copy number ratios
 form the raw .cel files of a GenomeWideSNP6.0 array - I was using CRMA1 but
 am now repeating the analysis using CRMA v2.
 I am putting all of the different tumour types either matched or unmatched
 with a germline sample in the same directory and all the normal samples in
 another directory.

This is fine, but note that did not need to put them in separate directories.

 I will then go through the processes of qulaity assesment, calibration
 crosstalk, normalization for probe sequence effect, probe summarization, and
 normalization of PCR fragment length effects.

 Do I need to calculate the raw copy numbers and turn these into log2 copy
 numbers?

I don't understand your question.

 How would I then calculate the copy numbers for
 1. Unpaired tumour samples - will need to be compared to a pooled reference
 from a particular tumpur type
 2. Paired samples?


It's hard to be more specific than what Henrik already said without
more details on your sample names and tumor types, and most
importantly on the design of your study.

I'll try for the unpaired analysis (your 1.)

I am assuming that you have two data sets:
- 'dsT' for the tumor samples,
- 'dsN' for the normal samples.

It seems that your concern is to use *tumor-type specific* sets of
normal samples.  Is that correct ?  See my remark below on the fact
that I'm not sure it's what you should do.

If so, then assuming that 'idxT1' contains the indices of all tumor
samples from a  particular tumor type in dsT, and 'idxN1' contains the
indices of normal samples from the same tumor type in dsN, you can do

dsN1 - extract(dsN, idxN1);  ## normal samples of tumor type 1
dsT1 - extract(dsT, idxT1);   ## tumor samples of tumor type 1

dfR1 - getAverageFile(dsN1);## pool of normal samples of tumor type 1
sm1 - CbsModel(dsT1, dfR1);

Then you can do

fit(sm1, chromosome=1, array=1, verbose=log);

to perform CBS segmentation and/or

rawCNs1 - extractRawCopyNumbers(sm1, array=1, chromosome=1)
plot(rawCns1)

to extract and plot raw copy numbers (independently of CBS).

And so on for each tumor type.

This should answer your 1.  However, I'm not sure that using
tumor-type specific sets of normal samples will give you better
results.  This depends in particular  on the following specific points
in your design:
- Are you normals  normal tissue samples blood samples ?
- Were all the tumor and normal microarrays done in the same lab, and
approximately at the same time ?  If so, combining all the normals
could be better.
One way to know which option is best (tumor-specific reference or
global reference) is to try both and compare the segmentation results
(e.g. using ChromosomeExplorer).

For your 2 (paired tumor/normal analysis), I think Henrik gave all the
necessary information already, but

assuming that 'idxT2' contains the indices of all tumor samples from a
 particular tumor type in dsT that have a paired normal, and 'idxN2'
contains the indices of these paired normal samples from the same
tumor type in dsN, further assuming that *the samples are in the same
order in the two sets of indices*, you can do

dsN2 - extract(dsN, idxN2);
dsT2 - extract(dsT, idxT2);

sm2 - CbsModel(dsT2, dsN2);

fit(sm2, chromosome=1, array=1, verbose=log);
rawCNs2 - extractRawCopyNumbers(sm2, array=1, chromosome=1)
plot(rawCNs2);

I hope this helps,

Pierre.


 Many thanks for your help

 On 18/07/2010 12:01, Ajanthah Sangaralingam a.sangaralin...@qmul.ac.uk
 wrote:

 Hi,

 Yes this is correct.

 Many thanks

 Ajanthah
 
 From: aroma-affymetrix@googlegroups.com [aroma-affymet...@googlegroups.com] 
 On
 Behalf Of Henrik Bengtsson [...@stat.berkeley.edu]
 Sent: Sunday, July 18, 2010 11:28 AM
 To: aroma-affymetrix
 Subject: Re: [aroma.affymetrix] Analysis of GenomeWideSNP6.0 data

 Hi.

 On Fri, Jul 16, 2010 at 11:13 AM, Ajanthah Sangaralingam
 a.sangaralin...@qmul.ac.uk wrote:
 Hi,

 I have been doing some paired total copy number analysis in aroma 
 afyymetrix.
 The dataset I have is complicated for haf the dataset I have reference
 samples, for the other half I will do an unpiared analysis.

 So, to make sure I don't misunderstand, you have an Affymetrix
 GenomeWideSNP_6 (GWS6) data set that contains tumors and for some, but
 not all of the you have matched normal samples, where matched normal
 mean a normal tissue or normal blood extract from the same patient as
 the tumor was taken.  Is this correct?

 I alos have data from many different tomor types not just one - I do not 
 have
 the sample number of samples from each type of tumor.

 My questions are:

 When doing a paired analysis - the normal and tumour data have there own
 directories and allelic cross talk calibration, summarization and PCR
 fragment length normlization is all done separately.

 It is 

Re: [aroma.affymetrix] Error need help(CdfFile$byChipType)

[Pierre Neuvial]

Hi,

Most probably you haven't put the required CDF file in the
corresponding annotationData/chipTypes/ directory.

Have you read the vignette http://aroma-project.org/node/38 ? This is
well explained there.

Also, similar versions of this question have been answered on this
list, see for example
  
http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/d992f2ca51e71774/8ba42bb7bdbf1b48

Best

Pierre.


Be sure to put the CDF file in your annotationData/chipTypes/XX/ where
XX is the platform you are using (e.g.  HuGene-1_0-st-v1 for Human
Gene 1.0 ST, HT_HG-U133_Plus_PM for the human PM plate arrays, etc.)

On Tue, Aug 3, 2010 at 2:27 PM, vish ashwin4bioinformat...@gmail.com wrote:

 I am really new to this aroma.affymetrix. I am trying to analyze
 HuGene-1_0-st-v1 array and interested in Quality control check/
 Assessment.
 when I am trying to run this command I am ending up with this error .
 Any help is greatly appreciated.

 cdf - AffymetrixCdfFile$byChipType(chipType, tags=r3)
 Error in list(`AffymetrixCdfFile$byChipType(chipType, tags = r3)` =
 environment,  :

 [2010-08-03 16:23:44] Exception: Could not locate a file for this chip
 type: HuGene-1_0-st-v1,r3
  at throw(Exception(...))
  at throw.default(Could not locate a file for this chip type: ,
 paste(c(chipType, tags), collapse = ,))
  at throw(Could not locate a file for this chip type: ,
 paste(c(chipType, tags), collapse = ,))
  at method(static, ...)
  at AffymetrixCdfFile$byChipType(chipType, tags = r3)

 Ashwin

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Re: [aroma.affymetrix] attach two data frames

[Pierre Neuvial]

Hi Viking,

Note that your question has nothing to do with aroma.* packages, so it
should not be posted on this list.

In this particular case, I think the function to use is Google search :)

http://www.google.com/search?q=combine+data+frame

Pierre


On Thu, Jul 15, 2010 at 10:52 AM, Liang Cheng vikingch...@gmail.com wrote:
 Hello,
 I have two data frames, and I want to combine them together, that means I
 want to put one after the bottom of the other.
 For example, I have a data frame x, y

 x:

 column name: A  B C
     1  1  3
     3  5  6
 y:

 column name:A  F  G
   3   9   1
    8  7   0

 I want to get a new data frame like this:

    A   B  C
   1    1   3
   3    5    6
   3    9    1
   87    0

 what function should I use?
 thanks a lot：）

 Viking

 --
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Re: [aroma.affymetrix] uncomplete extractDataFrame()

[Pierre Neuvial]

Salut Emilie,

On Thu, Jul 1, 2010 at 10:13 AM, EmilieT temilie...@gmail.com wrote:
 Hello,

 I am using your R framework with a set of Affymetrix SNP 6 data and I
 have a problem with the extractDataFrame function.
 The result is an incomplete matrix with row duplication.

 sessionInfo()
 R version 2.11.1 (2010-05-31)
 x86_64-apple-darwin9.8.0

 locale:
 [1] fr_FR.UTF-8/fr_FR.UTF-8/C/C/fr_FR.UTF-8/fr_FR.UTF-8

 attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods
 base

 other attached packages:
  [1] aroma.cn_0.5.0         aroma.affymetrix_1.6.0
 aroma.apd_0.1.7        affxparser_1.20.0      R.huge_0.2.0
  [6] aroma.core_1.6.0       matrixStats_0.2.1
 R.rsp_0.3.6            R.cache_0.3.0          R.filesets_0.8.2
 [11] digest_0.4.2           R.utils_1.4.0
 R.oo_1.7.2             aroma.light_1.16.0     R.methodsS3_1.2.0

 I use the standard doCRMAv2 function :
   ds - doCRMAv2(data,
 chipType=GenomeWideSNP_6,combineAlleles=FALSE);

 ds
 $total
 AromaUnitTotalCnBinarySet:
 Name: data
 Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
 Full name: data,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
 Number of files: 14
 Names: A,B, ..., C [14]
 Path (to the first file): totalAndFracBData/data,ACC,ra,-XY,BPN,-
 XY,AVG,FLN,-XY/GenomeWideSNP_6
 Total file size: 99.13 MB
 RAM: 0.02MB

 $fracB
 AromaUnitFracBCnBinarySet:
 Name: data
 Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
 Full name: data,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
 Number of files: 14
 Names: A,B, ..., C [14]
 Path (to the first file): totalAndFracBData/data,ACC,ra,-XY,BPN,-
 XY,AVG,FLN,-XY/GenomeWideSNP_6
 Total file size: 99.13 MB
 RAM: 0.02MB

 It seems to be impossible to use this 'ds' object (or ds$fracB or ds
 $total) as an entrance for the extractDataFrame() function.

Yes: this is because extractDataFrame is meant to extract *chip
effects* (http://aroma-project.org/howtos/extractDataFrame) in your
case total and allele-specific *intensities*, and your ds$total and
ds$fracB are already one step further in the analysis: they are
AromaUnit*CnBinaryFile:s.  For these you can use writeDataFrame
(http://aroma-project.org/howtos/writeDataFrame) as you seem to be
doing below.

 So I must do :

 rootPath - totalAndFracBData
 dataSet - data,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
 ds - AromaUnitFracBCnBinarySet$byName(dataSet, chipType=GenomeWideSNP_6, 
 paths=rootPath);
 ds
 AromaUnitFracBCnBinarySet:
 Name: data
 Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
 Full name: data,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY
 Number of files: 14
 Names: A,B, ..., C [14]
 Path (to the first file): totalAndFracBData/data,ACC,ra,-XY,BPN,-
 XY,AVG,FLN,-XY/GenomeWideSNP_6
 Total file size: 99.13 MB
 RAM: 0.02MB

You don't really to do this: your new 'ds' is exactly your previous
'ds$fracB' (more on this below).


 When I use the extractDataFrame function, I obtain the folowing
 object :

Below you are using writeDataFrame, not extractDataFrame. Right ?


 dfTxt - writeDataFrame(ds, columns=c(unitName, chromosome, position, 
 *))
 d - readDataFrame(dfTxt)
 str(d)
 'data.frame':   1857154 obs. of  17 variables:
  $ unitName                     : Factor w/ 71429 levels
 AFFX-5Q-123,..: 1 2 3 4 487 490 493 496 499 502 ...
  $ chromosome                : int  NA NA NA NA NA NA NA NA NA NA ...
  $ position                        : int  NA NA NA NA NA NA NA NA NA
 NA ...
  $ A,fracB                        : num  NA NA NA NA NA NA NA NA NA
 NA ...
  $ B,fracB                        : num  NA NA NA NA NA NA NA NA NA
 NA ...
  $ C,fracB                       : num  NA NA NA NA NA NA NA NA NA
 NA ...
  $ ...

 First of all, you can see that there is only the fracB columns. The
 first ds object had a total item, it seems to have been lost. The
 directory
 /totalAndFracBData/data,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY/GenomeWideSNP_6
 also contain the ,total.asb files. There is maybe a problem with
 my new 'ds' object (which refers to only 14 files).

Yes, this is expected because your new 'ds' has been created using

ds - AromaUnitFracBCnBinarySet$byName(dataSet,
chipType=GenomeWideSNP_6, paths=rootPath);

As the FracB indicates, this 'ds' only contains allele B fractions. You can do

totalDs - AromaUnitTotalCnBinarySet$byName(dataSet,
chipType=GenomeWideSNP_6, paths=rootPath);

to get the corresponding total CN data.


 There is also a problem of row duplication : you can see that the
 number of row is the same as Affymetrix SNP 6 number of units (so the
 result seems to be good).

Well, I've tried to reproduce what you have and I'm getting 200 rows:

 str(d);
'data.frame':   200 obs. of  5 variables:
 $ unitName   : Factor
w/ 50 levels AFFX-5Q-123,..: 1 2 3 4 487 490 493 496 499 502 ...
 $ chromosome : int
NA NA NA NA NA NA NA NA NA NA ...
 $ position   : int
NA NA NA NA NA NA NA NA NA NA ...
 $ STAIR_p_TCGA_Batch7_Affx_N_GenomeWideSNP_6_E03_238454,fracB: 

Re: [aroma.affymetrix] Microsoft Visual C++ Runtime Library

[Pierre Neuvial]

Hi,

Could you please report the output of sessionInfo() and traceback(),
and post a complete code example ?

Pierre

On Tue, Jun 29, 2010 at 10:09 AM, Liang Cheng vikingch...@gmail.com wrote:
 Hello everyone,
 I meet this error when I try to read 10 CEL files by using AffymetrixCelSet:

 the application has requested the runtime to terminate it in an unusaul way.

 Can someone help me？
 thanks a lot,
 Liang

 --
 When reporting problems on aroma.affymetrix, make sure 1) to run the latest
 version of the package, 2) to report the output of sessionInfo() and
 traceback(), and 3) to post a complete code example.


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Re: [aroma.affymetrix] Microsoft Visual C++ Runtime Library

[Pierre Neuvial]

Thanks, and when do you get an error ? Can you paste the error message
and the output of traceBack() ?

Pierre

On Thu, Jul 1, 2010 at 10:26 AM, Liang Cheng vikingch...@gmail.com wrote:
 Thank you, Pierre,
 the following is the sessionInfo and code:

 R version 2.11.0 (2010-04-22)
 i386-pc-mingw32
 locale:
 [1] LC_COLLATE=English_United States.1252
 [2] LC_CTYPE=English_United States.1252
 [3] LC_MONETARY=English_United States.1252
 [4] LC_NUMERIC=C
 [5] LC_TIME=English_United States.1252
 attached base packages:
 [1] stats graphics  grDevices utils datasets  methods   base
 other attached packages:
  [1] preprocessCore_1.10.0  aroma.affymetrix_1.6.0 aroma.apd_0.1.7
  [4] affxparser_1.20.0  R.huge_0.2.0   aroma.core_1.6.0
  [7] aroma.light_1.16.0 matrixStats_0.2.1  R.rsp_0.3.6
 [10] R.cache_0.3.0  R.filesets_0.8.2   digest_0.4.2
 [13] R.utils_1.4.2  R.oo_1.7.3 R.methodsS3_1.2.0

 Code:

  library(aroma.affymetrix)
 cs - AffymetrixCelSet$byName(1,
 chipType=Mapping250K_Nsp)
 qn - QuantileNormalization(cs)
 csQN - process(qn, verbose=TRUE)
 plm - RmaCnPlm(csQN, combineAlleles=TRUE, mergeStrands=TRUE)
 fit(plm, verbose=TRUE)
 ces - getChipEffectSet(plm)
 exData - extractDataFrame(ces, units=NULL, addNames=TRUE)
 write.table(exData,file=fileName.txt,row.names=FALSE)

 thank you very much,

 Liang


 2010/7/1 Pierre Neuvial pie...@stat.berkeley.edu

 Hi,

 Could you please report the output of sessionInfo() and traceback(),
 and post a complete code example ?

 Pierre

 On Tue, Jun 29, 2010 at 10:09 AM, Liang Cheng vikingch...@gmail.com
 wrote:
  Hello everyone,
  I meet this error when I try to read 10 CEL files by using
  AffymetrixCelSet:
 
  the application has requested the runtime to terminate it in an unusaul
  way.
 
  Can someone help me？
  thanks a lot,
  Liang
 
  --
  When reporting problems on aroma.affymetrix, make sure 1) to run the
  latest
  version of the package, 2) to report the output of sessionInfo() and
  traceback(), and 3) to post a complete code example.
 
 
  You received this message because you are subscribed to the Google
  Groups
  aroma.affymetrix group with website http://www.aroma-project.org/.
  To post to this group, send email to aroma-affymetrix@googlegroups.com
  To unsubscribe and other options, go to
  http://www.aroma-project.org/forum/
 

 --
 When reporting problems on aroma.affymetrix, make sure 1) to run the
 latest version of the package, 2) to report the output of sessionInfo() and
 traceback(), and 3) to post a complete code example.


 You received this message because you are subscribed to the Google Groups
 aroma.affymetrix group with website http://www.aroma-project.org/.
 To post to this group, send email to aroma-affymetrix@googlegroups.com
 To unsubscribe and other options, go to
 http://www.aroma-project.org/forum/

 --
 When reporting problems on aroma.affymetrix, make sure 1) to run the latest
 version of the package, 2) to report the output of sessionInfo() and
 traceback(), and 3) to post a complete code example.


 You received this message because you are subscribed to the Google Groups
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-- 
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version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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Re: [aroma.affymetrix] re: chipEffects getAverage = 0?

[Pierre Neuvial]

Hi Seth,

On Thu, Feb 18, 2010 at 5:32 AM, seth redmond
seth.redm...@imperial.ac.uk wrote:
 I seem to be having some trouble generating an average file for a chip
 effects set. I'm following the CRMA2 vignette (skipping the fragment lengths
 normalisation). The CES seems to be generated OK, but getAverage returns '0'
 for all values. Any ideas why? missing the frag-length normalisation
 shouldn't affect this should it?

No, it shouldn't. Can you post your entire script and your sessionInfo() ?

Best,

Pierre.

 thanks
 -s


 print(ces); print(ces[1]);
 CnChipEffectSet:
 Name: AgSNP01_set
 Tags: ACC,-XY,BPN,-XY,AVG,A+B
 Path: plmData/AgSNP01_set,ACC,-XY,BPN,-XY,AVG,A+B/Ag_SNP_1m520721
 Platform: Affymetrix
 Chip type: Ag_SNP_1m520721,monocell
 Number of arrays: 81
 Names: EROSE_p_MS_Pop_Struct_Bamako_Ag_SNP_1m520721_A01_458244,
 EROSE_p_MS_Pop_Struct_Bamako_Ag_SNP_1m520721_A02_458242, ...,
 SAGAS_p_MS_Pop_Pilot1_MM4
 g_SNP_1m520721_D08_445850
 Time period: 2010-02-16 16:39:47 -- 2010-02-16 16:40:00
 Total file size: 1240.10MB
 RAM: 0.15MB
 Parameters: (probeModel: chr pm, mergeStrands: logi TRUE, combineAlleles:
 logi TRUE)
 $Ag_2L_005857148
 $Ag_2L_005857148$AT
 $Ag_2L_005857148$AT$theta
       [,1]  [,2]  [,3]  [,4]  [,5]  [,6]  [,7]  [,8]  [,9] [,10] [,11] [,12]
 [1,] 40607 49887 58641 74699 73849 59042 57730 44588 56064 53004 47275 43394
      [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
 [1,] 48138 58073 41664 39946 24412 55460 49378 91170 60162 53812 38040 32548
      [,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36]
 [1,]  4639  6035 63732 62983 70399  8569 10699 56710 63548 40405 49868 33613
      [,37] [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48]
 [1,] 44585 20986 33751 49092 43146 42322 38705 30467 31034 23933 54582 32668
      [,49] [,50] [,51] [,52] [,53] [,54]  [,55] [,56] [,57] [,58] [,59]
 [,60]
 [1,] 28798 23453 65232 45382 65549 81326 172111 45896 33892 42695 61220
 27770
      [,61] [,62] [,63] [,64] [,65] [,66] [,67] [,68] [,69] [,70] [,71] [,72]
 [1,] 90138 36600 21338 30336 27390 37789 38993 33366 15584  2688 35110 36887
      [,73] [,74] [,75] [,76] [,77] [,78] [,79] [,80] [,81]
 [1,] 39633 37054 47837 47488 48989 36130 35849 20710 33560


 ceR - getAverageFile(ces, verbose=verbose);
 20100218 13:21:08|Retrieving average cell signals across 81 arrays...
  CnChipEffectFile:
  Name: .average-intensities-median-mad
  Tags: f2e3009e11cbfd8257aa2ba6118e5039
  Full name: .average-intensities-median-mad,f2e3009e11cbfd8257aa2ba6118e5039
  Pathname:
 plmData/AgSNP01_set,ACC,-XY,BPN,-XY,AVG,A+B/Ag_SNP_1m520721/.average-intensities-median-mad,f2e3009e11cbfd8257aa2ba6118e5039.CEL
  File size: 15.31 MB (16053637 bytes)
  RAM: 0.03 MB
  File format: v4 (binary; XDA)
  Platform: Affymetrix
  Chip type: Ag_SNP_1m520721,monocell
  Timestamp: 2010-02-16 16:41:57
  Parameters: (probeModel: chr pm, mergeStrands: logi TRUE, combineAlleles:
 logi TRUE)
 20100218 13:21:09|Retrieving average cell signals across 81 arrays...done
 print(ceR); print(ceR[1]);
 CnChipEffectFile:
 Name: .average-intensities-median-mad
 Tags: f2e3009e11cbfd8257aa2ba6118e5039
 Full name: .average-intensities-median-mad,f2e3009e11cbfd8257aa2ba6118e5039
 Pathname:
 plmData/AgSNP01_set,ACC,-XY,BPN,-XY,AVG,A+B/Ag_SNP_1m520721/.average-intensities-median-mad,f2e3009e11cbfd8257aa2ba6118e5039.CEL
 File size: 15.31 MB (16053637 bytes)
 RAM: 0.03 MB
 File format: v4 (binary; XDA)
 Platform: Affymetrix
 Chip type: Ag_SNP_1m520721,monocell
 Timestamp: 2010-02-16 16:41:57
 Parameters: (probeModel: chr pm, mergeStrands: logi TRUE, combineAlleles:
 logi TRUE)
 $Ag_2L_005857148
 $Ag_2L_005857148$AT
 $Ag_2L_005857148$AT$theta
 [1] 0



 --

 Seth Redmond

   Scientific Programmer, VectorBase

   Kafatos / Christophides Groups

   Div. Cell and Molecular Biology

   Imperial College, London

 seth.redm...@imperial.ac.uk

 --

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Re: [aroma.affymetrix] basic problem with AffymetrixCelSet

[Pierre Neuvial]

Hi Mike,

Did you try to (g)unzip all your CEL files in
rawData/GSE15907/MoGene-1_0-st-v1 ?

I don't think that aroma.affymetrix can handle gzipped CEL files.

Also, please report your sessionInfo()

Best

Pierre.

On Thu, Jan 28, 2010 at 8:45 AM, mike dewar mikede...@gmail.com wrote:
 Hi,

 First of all: apologies if I'm missing something obvious.

 I'm trying to read a set of CEL files from the ImmGen project,
 (GSE15907). I'm following the document at
 http://groups.google.com/group/aroma-affymetrix/web/gene-1-0-st-array-analysis
 but I'm running into an error I can't interpret. Any help would be
 most appreciated!

 My folder structure is the following:

 /Users/mike/Data/Immgen
   |-annotationData
   |---chipTypes
   |-MoGene-1_0-st-v1    --- in here is MoGene-1_0-st-v1,r3.cdf
   |---samples
   |-rawData
   |---GSE15907
   |-MoGene-1_0-st-v1    --- in here are lots of gzipped CEL
 files

 The code I'm using is

 library('aroma.affymetrix')
 setwd(/Users/mike/Data/Immgen)
 cdf - AffymetrixCdfFile$byChipType(MoGene-1_0-st-v1,tags=r3)
 cs - AffymetrixCelSet$byName(GSE15907,cdf=cdf)
 print(cs)

 The error I get is

 [2010-01-28 11:41:18] Exception: Argument 'x' is of length 1 although
 the range ([0,0]) implies that is should be empty.
  at throw(Exception(...))
  at throw.default(sprintf(Argument 'x' is of length %d although the
 range ([%s
  at throw(sprintf(Argument 'x' is of length %d although the range
 ([%s,%s]) im
  at getIndices.Arguments(static, ..., length = length)
  at getIndices(static, ..., length = length)
  at method(static, ...)
  at Arguments$getIndex(idx, max = n)
  at getFile.GenericDataFileSet(this, 1)
  at getFile(this, 1)
  at getUnitNamesFile.AffymetrixCelSet(this)
  at getUnitNamesFile(this)
  at getChipType.AffymetrixCelSet(this)
  at getChipType(this)
  at sprintf(Chip type: %s, getChipType(this))
  at as.character.AffymetrixCelSet(x)
  at as.character(x)
  at print(as.character(x))
  at print.Object(cs)
  at print(cs)
 Calls: print ... getIndices.Arguments - throw - throw.default -
 throw - throw.Exception
 Execution halted

 Has anyone got any ideas as to where I'm going wrong?

 Cheers,

 Mike Dewar

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 version of the package, 2) to report the output of sessionInfo() and 
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version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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Re: [aroma.affymetrix] matching affy SNP names with their “rs” names

[Pierre Neuvial]

Hi Max !

Short reply: you can get this information from the NetAffx annotation
files.  For example, for GenomeWideSNP_6, the mapping can be retrieved
from

  
http://www.affymetrix.com/Auth/analysis/downloads/na29/genotyping/GenomeWideSNP_6.na29.annot.csv.zip

The first two columns are the SNP id and the rs id. I'll try to add a
HowTo on this to the aroma-project.org website soon.

Best,

Pierre

On Wed, Jan 27, 2010 at 5:20 PM, Max Moldovan max.moldo...@gmail.com wrote:
 Hi People,

 I am extracting unit names from specific chromosome over specific
 region (x,y) e.g.:

 gi - getGenomeInformation(cdf)
 units - getUnitsOnChromosome(gi, chromosome=2, region=c(x,y))
 unit_names - getUnitNames(cdf, unit=units)

 “unit_names” will contain something like SNP_A-2243961 and CN_195975
 for SNPs and copy number probes, respectively.

 It is possible to go to a genome browser (e.g. UCSC) and pool “rs”
 names for SNPs.

 The question is, can I match the affy names of SNPs (e.g.
 SNP_A-2243961) to their “rs” names (i.e. rs17013229) using annotation
 information within aroma.affy?

 Thanks and best wishes

 Max

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[aroma.affymetrix] 'affymetrix_calvin_exceptions::FileNotOpenException' [Was: Re: Total CNs analysis]

[Pierre Neuvial]

Hi Anguraj,

[cc'ing the mailing list in case other people run into the same problem]

I can reproduce the error.  Pasting the error message you got in the
search box of aroma.affymetrix's discussion page I found this thread

http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/13b581ecc47f0b91

which suggests one of the CEL files may be corrupt.

Narrowing it down I found that the error does not come from the tumor samples:

 csT - AffymetrixCelSet$byName(dataSet, cdf=cdf, pattern=GSM, 
 verbose=verbose);
 print(csT);

AffymetrixCelSet:
Name: GSE16619Data
Tags:
Path: rawData/GSE16619Data/GenomeWideSNP_5
Platform: Affymetrix
Chip type: GenomeWideSNP_5,Full,r2
Number of arrays: 119
Names: GSM417171_BC43, GSM417172_BC44, ..., GSM417386_BC161
Time period: 2008-01-16 17:49:01 -- 2008-04-18 22:44:14
Total file size: 5333.27MB
RAM: 0.16MB

but from the normal samples

 csN - AffymetrixCelSet$byName(dataSet, cdf=cdf, pattern=NA, 
 verbose=verbose);
 print(csN)
terminate called after throwing an instance of
'affymetrix_calvin_exceptions::FileNotOpenException'

I've had a quick look at the file sizes and they seem correct.

I suggest you try the following:
1) store the tumor and normal samples in two different data set
directories, named after their GEO ID:

rawData/
  dataSet1/
GenomeWideSNP_5/
  *.CEL
  dataSet2/
GenomeWideSNP_5/
  *.CEL

That's what they are: two different data sets. There is no reason to
store them in the same folder.

2) Now you can start normalizing the tumor data set without loosing more time.
3) Troubleshoot the problem with the CEL files from the normal data set:

I know very little about CEL files but the first lines of the files
don't look good, especially the
text/ascii%affymetrix-algorithm-param- thing and the fact that part
of the header seems to be missing:

bash-3.00$ head NA06985_Op1_011206_VnV_D10_r1.CEL

;?ffymetrix-calvin-intensity6030075-1192819521-006334-018467-41en-US#%affymetrix-algorithm-param-Percentile75
text/ascii%affymetrix-algorithm-param-CellMargin4
text/asciiaffymetrix-algorithm-param-OutlierHigh1.500
text/ascii%affymetrix-algorithm-param-OutlierLow1.004
text/ascii%affymetrix-algorithm-param-AlgVersion6.0
text/ascii(affymetrix-algorithm-param-FixedCellSizeTRUE
text/ascii+affymetrix-algorithm-param-FullFeatureWidth7
text/ascii,affymetrix-algorithm-param-FullFeatureHeight7
text/ascii4affymetrix-algorithm-param-IgnoreOutliersInShiftRowsFALSE
text/ascii,affymetrix-algorithm-param-FeatureExtractionTRUE

Does this help ?

Pierre.

On Fri, Jan 15, 2010 at 10:26 AM, Anguraj Sadanandam
sadana...@gmail.com wrote:
 Hi Pierre,

  Sorry to bother you again.

  May be a simple bug, but I am getting this error for the same SNP5 data 
 analysis.

 print(cs);
 terminate called after throwing an instance of 
 'affymetrix_calvin_exceptions::Fi
 leNotOpenException'

  I hope you know where to look for the output file.

  THanks,

 Anguraj

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Re: [aroma.affymetrix] custom CDF

[Pierre Neuvial]

Hi Zaid,

Does your file satisfy the requirements detailed on the corresponding
help page ?

http://groups.google.com/group/aroma-affymetrix/web/creating-cdf-files-from-scratch

Pierre

On Wed, Dec 9, 2009 at 4:18 PM, zaid z...@genomedx.com wrote:
 Hello,

 I'm trying to create a custom CDF file from a flat file uisng the R
 script provided in this group (flat2Cdf()).

 I'm running into errors such as incorrect number of columns, integer
 not found etc.

 Is there a standard flat file structure required? Or are there any
 flat files available for download?
 I just want to try the script and have a standard structure to work
 with.


 Thanks for the help.

 Z

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Re: [aroma.affymetrix] GenomeGraphs and BioMart

[Pierre Neuvial]

Hi Maria,

I think you should report this problem to the Bioconductor mailing
list instead, as it has to do with BioMart and GenomeGraphs, not with
aroma.*

Cheers

Pierre.

On Fri, Dec 4, 2009 at 5:14 AM, Maria Traka maria.tr...@bbsrc.ac.uk wrote:
 I am running GenomeGraphs with my exon data and i get the following
 error message. I have used this in the past sucessfully so not sure
 what has changed now...
 Can you help???
 Thanks,
 Maria

 gene-new(Gene,id=ENSMUSG0047517, type=ensembl_gene_id, 
 biomart=mart)

 V1
 1                          !DOCTYPE HTML PUBLIC -//W3C//DTD HTML
 4.01 Transitional//EN http://www.w3.org/TR/html4/loose.dtd;
 2                                            HTMLHEADMETA HTTP-
 EQUIV=Content-Type CONTENT=text/html; charset=iso-8859-1
 3
 TITLEERROR: The requested URL could not be retrieved/TITLE
 4  STYLE type=text/css!--BODY{background-color:#ff;font-
 family:verdana,sans-serif}PRE{font-family:sans-serif}--/STYLE
 5
 /HEADBODY
 6
 H1ERROR/H1
 7
 H2The requested URL could not be retrieved/H2
 8
 HR noshade size=1px
 9
 P
 10
 While trying to process the request:
 11
 PRE
 12
 POST /biomart/martservice? HTTP/1.1
 13
 Host: www.biomart.org
 14
 Accept: */*
 15
 Proxy-Connection: Keep-Alive
 16
 Content-Length: 680
 17
 Expect: 100-continue
 18                                           Content-Type: multipart/
 form-data; boundary=5c094063af6b
 19
 /PRE
 20
 P
 21
 The following error was encountered:
 22
 UL
 23
 LI
 24
 STRONG
 25
 Invalid Request
 26
 /STRONG
 27
 /UL
 28
 P
 29                                                                Some
 aspect of the HTTP Request is invalid.  Possible problems:
 30
 UL
 31
 LIMissing or unknown request method
 32
 LIMissing URL
 33
 LIMissing HTTP Identifier (HTTP/1.0)
 34
 LIRequest is too large
 35
 LIContent-Length missing for POST or PUT requests
 36
 LIIllegal character in hostname; underscores are not allowed
 37
 /UL
 38                                  PYour cache administrator is A
 HREF=mailto:webm...@bbsrc.ac.uk;webm...@bbsrc.ac.uk/A.
 39
 BR clear=all
 40
 HR noshade size=1px
 41
 ADDRESS
 42                                          Generated Fri, 04 Dec 2009
 13:11:25 GMT by BBSRC-wwwcache-service (squid/2.7.STABLE6)
 43
 /ADDRESS
 44
 /BODY/HTML
 Error in getBM(c(ensembl_gene_id, ensembl_transcript_id,
 ensembl_exon_id,  :
  The query to the BioMart webservice returned an invalid result: the
 number of columns in the result table does not equal the number of
 attributes in the query. Please report this to the mailing list.

 sessionInfo()
 R version 2.9.0 (2009-04-17)
 i386-pc-mingw32

 locale:
 LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.
 1252;LC_MONETARY=English_United Kingdom.
 1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252

 attached base packages:
 [1] grid      stats     graphics  grDevices datasets  utils
 methods   base

 other attached packages:
  [1] RCurl_0.98-1           bitops_1.0-4.1
 GenomeGraphs_1.4.1     biomaRt_2.0.0          limma_2.18.1
 aroma.affymetrix_1.1.0
  [7] aroma.apd_0.1.3        R.huge_0.1.7
 affxparser_1.16.0      aroma.core_1.1.0       aroma.light_1.13.2
 matrixStats_0.1.4
 [13] R.rsp_0.3.4            R.filesets_0.5.1
 digest_0.3.1           R.cache_0.1.7          R.utils_1.1.6
 R.oo_1.4.6
 [19] R.methodsS3_1.0.3      RWinEdt_1.8-1

 loaded via a namespace (and not attached):
 [1] XML_2.3-0


 --
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 version of the package, 2) to report the output of sessionInfo() and 
 traceback(), and 3) to post a complete code example.


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Re: [aroma.affymetrix] where is the vignitte for FIRMA?

[Pierre Neuvial]

Hi Wenhong,

Here is the Human Exon Array Analysis vignette:

http://groups.google.com/group/aroma-affymetrix/web/human-exon-array-analysis

It's listed with the other help pages:
http://groups.google.com/group/aroma-affymetrix/web

Best,

Pierre

On Fri, Nov 6, 2009 at 4:27 PM, Wenhong wben...@gmail.com wrote:
 Hi
 Just starting using Aroma.Affymetrix and FIRMA to analyze Exon array.
 Can somebody point me the help or vignitte for the packages? Thanks
 Wenhong

 --
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[aroma.affymetrix] Re: Exception: Unknown arguments: cdf, checkChipType

[Pierre Neuvial]

Hi Carol,

On Mon, Oct 12, 2009 at 9:15 AM, cjb carol.b...@gmail.com wrote:

 Hi all,

 I am following along with the Gene 1.0 ST Vignette:
 http://groups.google.com/group/aroma-affymetrix/web/gene-1-0-st-array-analysis

 and with Henrik's August 7, 2007 aroma.affymetrix tutorial.

 All goes well until  I try to do background correction or quantile
 normalization.

 When I try to do either background correction or quantile
 normalization I get a similar error:
 Exception: Unknown arguments: cdf, checkChipType

 When I look in my working directory, there is a probeData directory
 that has been created. And within that directory, two directories with
 tags.

 MGH_Data\probeData\MGH09,QN\MoGene-1_0-st-v1

 MGH_Data\probeData\MGH09,RBC\MoGene-1_0-st-v1

 1. Creating the cdf and cs objects:

 cdf - AffymetrixCdfFile$byChipType(MoGene-1_0-st-v1)
 cdf
 AffymetrixCdfFile:
 Path: annotationData/chipTypes/MoGene-1_0-st-v1
 Filename: MoGene-1_0-st-v1.cdf
 Filesize: 67.42MB
 Chip type: MoGene-1_0-st-v1
 RAM: 0.00MB
 File format: v3 (text; ASCII)
 Dimension: 1050x1050
 Number of cells: 1102500
 Number of units: 35512
 Cells per unit: 31.05
 Number of QC units: 1

 cs - AffymetrixCelSet$byName(MGH09,chipType=MoGene-1_0-st-v1)
 print(cs)
 AffymetrixCelSet:
 Name: MGH09
 Tags:
 Path: rawData/MGH09/MoGene-1_0-st-v1
 Platform: Affymetrix
 Chip type: MoGene-1_0-st-v1
 Number of arrays: 26
 Names: J001_3_11.5, J001_4_11.5, ..., J010_4_16.5
 Time period: 2009-09-23 17:51:49 -- 2009-09-23 21:45:31
 Total file size: 275.06MB
 RAM: 0.02MB


Have you tried

cs - AffymetrixCelSet$byName(MGH09, cdf=cdf)

instead, as in the Gene 1.0 ST Vignette you are citing ?

Also, are you using the latest versions of the packages ? Please give
the output of sessionInfo() so that we can figure this out.

Best,

Pierre.


 2. RmaBackgroundCorrection(s) Error:

 bc - RmaBackgroundCorrection(cs)
 csBC - process(bc, verbose=verbose)
 Background correcting data set...

 Error in list(`process(bc, verbose = verbose)` = environment,
 `process.RmaBackgroundCorrection(bc, verbose = verbose)` =
 environment,  :

 [2009-10-12 11:49:04] Exception: Unknown arguments: cdf, checkChipType
  at throw(Exception(...))
  at throw.default(Unknown arguments: , argsStr)
  at throw(Unknown arguments: , argsStr)
  at GenericDataFileSet(files = files, ...)
  at extend(GenericDataFileSet(files = files, ...),
 AromaMicroarrayDataSet)
  at AromaMicroarrayDataSet(files = files, ...)
  at extend(AromaMicroarrayDataSet(files = files, ...), c
 (AffymetrixFileSet, uses(AromaPlatformI
  at AffymetrixFileSet(files = files, ...)
  at extend(AffymetrixFileSet(files = files, ...), AffymetrixCelSet,
 `cached:.intensities` = NULL
  at this(...)
  at newInstance.Class(clazz, ...)
  at newInstance(clazz, ...)
  at newInstance.Object(static, files, ...)
  at newInstance(static, files, ...)
  at method(static, ...)
  at staticMethod(path = probeData/MGH09,RBC/MoGene-1_0-st-v1,
 pattern = ^[^.].*[.](CEL|cel)$,
  at do.call(staticMethod, args = args)
  at getOutputDataSet0.AromaTransform(this, ..., verbose
 Background correcting data set...done


 3. QuantileNormalization(cs) Error:

 qn -QuantileNormalization(cs)
 qn
 Error in list(`print(NA)` = environment, `print.Object(NA)` =
 environment,  :

 [2009-10-12 11:33:42] Exception: Unknown arguments: cdf, checkChipType
  at throw(Exception(...))
  at throw.default(Unknown arguments: , argsStr)
  at throw(Unknown arguments: , argsStr)
  at GenericDataFileSet(files = files, ...)
  at extend(GenericDataFileSet(files = files, ...),
 AromaMicroarrayDataSet)
  at AromaMicroarrayDataSet(files = files, ...)
  at extend(AromaMicroarrayDataSet(files = files, ...), c
 (AffymetrixFileSet, u
  at AffymetrixFileSet(files = files, ...)
  at extend(AffymetrixFileSet(files = files, ...), AffymetrixCelSet,
 `cached:.
  at this(...)
  at newInstance.Class(clazz, ...)
  at newInstance(clazz, ...)
  at newInstance.Object(static, files, ...)
  at newInstance(static, files, ...)
  at method(static, ...)
  at staticMethod(path = probeData/MGH09,QN/MoGene-1_0-st-v1,
 pattern = ^[^.]
  at do.call(staticMethod, args = args)


 


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[aroma.affymetrix] Re: Correspondence between aroma alleles and affy annotation

[Pierre Neuvial]

Hi,

On Wed, Sep 16, 2009 at 2:43 AM, marco mazu.c...@gmail.com wrote:

 Hi Pierre,

  I am following the CRMA2 vignette, so I am using the
 GenomeWideSNP_6,Full.cdf.
 At the same time I extracted the Allele A and B from the .csv
 annotation file provided by affy (GenomeWideSNP_6.na26.annot.csv)

FYI: the current version on NetAffx website is
GenomeWideSNP_6.na29.annot.csv, see

http://www.affymetrix.com/products_services/arrays/specific/genome_wide_snp6/genome_wide_snp_6.affx#1_4

 I guess that the .cdf and the .csv match.

Not really, as strange as it can sound; see below.

 So my question is if the alleleB of aroma is the allele B of affy. Is
 that the case ?


Yes, it is: aroma.affymetrix uses allele definitions of the cdf you
are working with, and you are working with Affy's cdf.

To answer your original question, which I think I've now understood:
you want to use the strand information, which is also in NetAffx
files: whenever the strand is - you have to swap what the cdf (or
aroma.affymetrix) calls allele A and allele B to make it consistent
with the allele A and allele B definition in the netAffx file.

If you don't do this, then the allele definition of the cdf does not
match that of NetAffx (even if you take the direction information
from the cdf into account, but that's another story). It took me quite
a while to figure this out when I first had to.

I hope this will help you.

Best,

Pierre.


 thanks a lot for the help!

 Best Regards

 Marco


 On Sep 16, 6:56 am, Pierre Neuvial pie...@stat.berkeley.edu wrote:
 Hi Marco,

 In case you haven't solved your problem yet...

 I think they should be the same if you have analyzed your data using
 one of the CDF provided by Affymetrix, which is most likely.
 What are you calling the affy annotation file for the SNP6.0 ? What
 CDF have you used ?

 Best,

 Pierre.

 On Mon, Sep 7, 2009 at 1:47 AM, marco mazu.c...@gmail.com wrote:

  Dear Henrik,

   is there a correspondence between what in Aroma is called ALLELE
  B (for example in extractTotalAndFreqB) and the ALLELE B in the
  affy annotation file for the SNP6.0 ?

  I would like to compare the caucasian frequencies as declared by affy
  with the frequencies estimated by pooling a ctrl cohort but it seems
  to me that the two B do not correspond to each other.  Is there any
  way to correspond the alleles?

  Best Regards

  Marco
 


--~--~-~--~~~---~--~~
When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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[aroma.affymetrix] Re: Correspondence between aroma alleles and affy annotation

[Pierre Neuvial]

Hi Marco,

In case you haven't solved your problem yet...

I think they should be the same if you have analyzed your data using
one of the CDF provided by Affymetrix, which is most likely.
What are you calling the affy annotation file for the SNP6.0 ? What
CDF have you used ?

Best,

Pierre.


On Mon, Sep 7, 2009 at 1:47 AM, marco mazu.c...@gmail.com wrote:

 Dear Henrik,

  is there a correspondence between what in Aroma is called ALLELE
 B (for example in extractTotalAndFreqB) and the ALLELE B in the
 affy annotation file for the SNP6.0 ?

 I would like to compare the caucasian frequencies as declared by affy
 with the frequencies estimated by pooling a ctrl cohort but it seems
 to me that the two B do not correspond to each other.  Is there any
 way to correspond the alleles?


 Best Regards

 Marco

 


--~--~-~--~~~---~--~~
When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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[aroma.affymetrix] Re: Log2 data

[Pierre Neuvial]

Hi David,

First a comment on your previous post: I understand you've been using
of the code of the Total copy number vignette

http://groups.google.com/group/aroma-affymetrix/web/total-copy-number-analysis

in which quantile normalization is used. If you read between the code
lines, you will see the following comment:

Comment: In Bengtsson et al. (2008), we show that it is better to do
allelic-crosstalk calibration and use quantile normalization as an
optional follow-up step.  However, since this example was prepared
before those results we concluded, we here only show how to perform
the quantile normalization.  Please see other vignette for the GWS6
chip type to see how to do allelic-crosstalk calibration.

This means replacing:

qn - QuantileNormalization(cs)
csN - process(qn, verbose=log)

by:

acc - AllelicCrosstalkCalibration(csR, model=CRMAv2)
csC - process(acc, verbose=log)
bpn - BasePositionNormalization(csC, target=zero)
csN - process(bpn, verbose=log)

FYI this page gives you the last version of the normalization and
summarization steps:
http://groups.google.com/group/aroma-affymetrix/web/code-snippets

In short, there are (at least) two good reasons for doing this:
1. you will be correcting the cause rather than the symptom
(sounds like Henrik is talking...).
2. it makes this step a single array step, which is a good point for
the discussion below.

See the CRMAv1 and v2 papers for more details:

Bengtsson, H.; Irizarry, R. A.; Carvalho, B.  Speed, T. P. Estimation
and assessment of raw copy numbers at the single locus level.
Bioinformatics, 2008, 24, 759-767. (CRMA v1 paper)
http://bioinformatics.oxfordjournals.org/cgi/content/full/24/6/759

Bengtsson, H.; Wirapati, P.  Speed, T. P. A single-array
preprocessing method for estimating full-resolution raw copy numbers
from all Affymetrix genotyping arrays including GenomeWideSNP 5  6.
Bioinformatics, 2009 (accepted). (CRMA v2 paper)
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp371v1

See below for a reply to your question.

On Wed, Aug 12, 2009 at 7:02 PM, Daviddaescarc...@gmail.com wrote:

 Thanks for the replay Pierre!

 I have the following:
 27 tumors
 38 Controls

 And I wonder the appropiate proccess design:

 Should I analize at the sametime, controls and tumors?

 or should I analize them individually? first, the set of tumors and
 then the set of controls.

 Finally, in order to obtain the log2ratio and considering both sets,
 what could be the best?

My short answer is you should analyze them all at the same time. By
analyze I mean normalize and summarize.

FYI: In the code you have posted there are two multi array steps:
quantile normalization and RMA summarization. Note that if you follow
the CRMAv2 snippet for 10-500K (at
http://groups.google.com/group/aroma-affymetrix/web/code-snippets) as
I've suggested above then the only multi-array step is the RMA
summarization.

At this stage I strongly suggest that you check what the densities of
signal intensities look like before and after normalization, using
'plotDensity'.

For the segmentation, assuming that cesNList is a list of two chip
types with 27+38 arrays in each, you can split them into one list for
tumors and one list for controls:

cesNListT - lapply(cesNList, extract, 1:27) ## assuming the first 27 are tumors
cesNListC - lapply(cesNList, extract, 27+1:38) ## assuming the last
27 are controls

and define your GladModel as

glad - GladModel(cesNListT, cesNListC) ## add all your favorite
options for GLAD here

This way cesNListC will be averaged to build a reference array Then
you can proceed as before and this reference array will be used to
calculate log-ratios and perform segmentation.

Cheers,

Pierre.


 Thanks again!

 David

 On Aug 11, 9:22 am, Pierre Neuvial pie...@stat.berkeley.edu wrote:
 Hi David,

 Your code seems to be correct, but see remarks below.



 On Fri, Jul 24, 2009 at 6:39 PM, Daviddaescarc...@gmail.com wrote:

  Hi, to everyone!

  I working with a set of 27 Cervican Cancer tumors using Affy 100k. I
  would like to get the log2 value for each SNP.

  I´m running the vignette (Everything runs just fine):

  library(aroma.affymetrix)
  verbose - Arguments$getVerbose(-8)
  timestampOn(verbose)
  name - oscar
  chipTypes - c(Mapping50K_Hind240, Mapping50K_Xba240)
  cdfs - lapply(chipTypes, FUN=function(chipType) {  AffymetrixCdfFile
  $byChipType(chipType)  })
  print(cdfs)
  gis - lapply(cdfs, getGenomeInformation)
  print(gis)
  sis - lapply(cdfs, getSnpInformation)
  print(sis)
  cesNList - list()

  chipType - chipTypes[1]
  cs - AffymetrixCelSet$byName(name, chipType=chipType)
  cs - extract(cs, !isDuplicated(cs))
  print(cs)
  qn - QuantileNormalization(cs)
  print(qn)
  csN - process(qn, verbose=-20)
  plm - RmaCnPlm(csN, combineAlleles=TRUE, mergeStrands=TRUE)
  print(plm)
  fit(plm, verbose=-20)
  ces - getChipEffectSet(plm)
  fln - FragmentLengthNormalization(ces)
  print(fln)
  cesNList[[chipType]] - process(fln, verbose

[aroma.affymetrix] Re: Exception: The fit function for requested RMA PLM flavor failed: affyPLM

[Pierre Neuvial]

Hi Mark,

It works as expected now. Thanks a lot for you extra-quick reply.

Pierre

On Thu, Aug 6, 2009 at 11:27 PM, Mark Robinsonmrobin...@wehi.edu.au wrote:

 Hi Pierre.

 It looks like your version of 'preprocessCore' is VERY outdated.
 Version 1.6.0 is the one that should go with 2.9.x (BioC 2.4) and you
 have 1.0.0 ...

 Cheers,
 Mark


 On 07/08/2009, at 7:23 AM, Pierre Neuvial wrote:


 Hi,

 I'm having trouble analyzing a set of 250K SNP arrays using the CRMAv2
 code from http://groups.google.com/group/aroma-affymetrix/web/code-snippets
 :
 I've got an error at the summarization step:

 plm - RmaCnPlm(csN, mergeStrands=TRUE, combineAlleles=TRUE)
 fit(plm, verbose=log)

 20090806 12:42:04|  Identifying non-fitted units in chip-effect
 file...done
 20090806 12:42:04| Identifying non-estimated units...done
 20090806 12:42:04| Getting model fit for 262338 units.
 Loading required package: preprocessCore
 simpleError in rmaModel(y): SET_VECTOR_ELT() can only be applied to a
 'list', not a 'character'
 Error in list(`source(R/CRMAv2.R)` = environment,
 `eval.with.vis(ei, envir)` = environment,  :

 [2009-08-06 12:42:04] Exception: The fit function for requested RMA
 PLM flavor failed: affyPLM
  at throw(Exception(...))
  at throw.default(The fit function for requested RMA PLM flavor
 failed: , fla
  at throw(The fit function for requested RMA PLM flavor failed: ,
 flavor)
  at getFitUnitGroupFunction.RmaPlm(this, ...)
  at getFitUnitGroupFunction(this, ...)
  at getFitUnitFunction.CnPlm(this)
  at getFitUnitFunction(this)
  at fit.ProbeLevelModel(plm, verbose = log)
  at fit(plm, verbose = log)
  at eval.with.vis(expr, envir, enclos)
  at eval.with.vis(ei, envir)
  at source(R/CRMAv2.R)
 20090806 12:42:04|Fitting model of class RmaCnPlm:...done

 From previous discussions on the list I understand this could come
 from recent modifications to preprocessCore.
 It could also come from the fact that I am using R 2.9.0 and cannot
 switch to R 2.9.1 quickly right now.

 Cheers,

 Pierre.

 traceback()
 13: throw.Exception(Exception(...))
 12: throw(Exception(...))
 11: throw.default(The fit function for requested RMA PLM flavor
 failed: ,
        flavor)
 10: throw(The fit function for requested RMA PLM flavor failed: ,
        flavor)
 9: getFitUnitGroupFunction.RmaPlm(this, ...)
 8: getFitUnitGroupFunction(this, ...)
 7: getFitUnitFunction.CnPlm(this)
 6: getFitUnitFunction(this)
 5: fit.ProbeLevelModel(plm, verbose = log)
 4: fit(plm, verbose = log)
 3: eval.with.vis(expr, envir, enclos)
 2: eval.with.vis(ei, envir)
 1: source(R/CRMAv2.R)
 sessionInfo()
 R version 2.9.0 (2009-04-17)
 x86_64-redhat-linux-gnu

 locale:
 LC_CTYPE
 =
 en_US
 .UTF
 -8
 ;LC_NUMERIC
 =
 C
 ;LC_TIME
 =
 en_US
 .UTF
 -8
 ;LC_COLLATE
 =
 en_US
 .UTF
 -8
 ;LC_MONETARY
 =
 C
 ;LC_MESSAGES
 =
 en_US
 .UTF
 -8
 ;LC_PAPER
 =
 en_US
 .UTF
 -8
 ;LC_NAME
 =
 C
 ;LC_ADDRESS
 =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

 attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base

 other attached packages:
 [1] preprocessCore_1.0.0   aroma.affymetrix_1.1.0 aroma.apd_0.1.6
 [4] R.huge_0.1.8           affxparser_1.16.0      aroma.core_1.1.2
 [7] aroma.light_1.12.2     matrixStats_0.1.6      R.rsp_0.3.4
 [10] R.filesets_0.5.2       digest_0.3.1           R.cache_0.1.7
 [13] R.utils_1.1.7          R.oo_1.4.8             R.methodsS3_1.0.3


 

 --
 Mark Robinson, PhD (Melb)
 Epigenetics Laboratory, Garvan
 Bioinformatics Division, WEHI
 e: m.robin...@garvan.org.au
 e: mrobin...@wehi.edu.au
 p: +61 (0)3 9345 2628
 f: +61 (0)3 9347 0852
 --






 


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traceback(), and 3) to post a complete code example.


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[aroma.affymetrix] Re: Copy numbers using CBS

[Pierre Neuvial]

Hi Suman,

You can also use writeRegions directly, as in:

writeRegions(cbs, chromosomes=22, verbose=verbose)

This won't generate the ChromosomeExplorer report as in the code in my
previous post, but it will create the .xls file with copy number
regions.

Cheers,

Pierre.

On Sat, Jul 25, 2009 at 7:28 PM, Pierre Neuvialpie...@stat.berkeley.edu wrote:
 Hi Suman,

 I think the easiest way to get the segmentation results into a text
 file is to use the code at the bottom of the Total Copy Number
 analysis vignette:

 http://groups.google.com/group/aroma-affymetrix/web/total-copy-number-analysis-6-0

 Specifically, if cesN is your CnChipEffectSet, you can do:

 cbs - CbsModel(cesN)
 ce - ChromosomeExplorer(cbs)
 process(ce, chromosomes=22, verbose=verbose)

 (here I'm using 'chromosomes=22' to do a quick analysis of this
 chromosome only but you can analyze several or all of them at the same
 time.) This will create not only the .xdr files you mentioned but also
 a '.xls' file in the folder cbsData/dataSet/chipType, that
 contains the segmentation results.

 Note that this file is actually a tab delimited text file, although
 its extension is .xls (so that it can be opened by Excel directly).

 Hope this helps,

 Pierre.

 FYI, .xdr files are binary files that you can load using 'loadObject'.

 On Fri, Jul 24, 2009 at 5:27 PM, Sumansuman.duvv...@gmail.com wrote:

 I used the fit() function now to output the segmentation output to
 cbsData folder. The output files are in .xdr format. Is there a way to
 convert them to text format or read them back in using R?

 On Jul 23, 3:50 pm, Suman suman.duvv...@gmail.com wrote:
 Hi,

 I used the cbsmodel() function to perform the cbs on the 250k chip
 array data

 cbs-cbsModel(cesN)

 How do I write the segmentation results to a text file? Is there an
 underlying function?

 Any pointers will be helpful

 Thanks,
 Suman
 



--~--~-~--~~~---~--~~
When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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[aroma.affymetrix] Re: cRMA v2

[Pierre Neuvial]

Hi ZZ,

First, could you please sign with an explicit name (and possibly
affiliation) or write using an explicit email address ? I (we) think
that's the least that can be expected from someone asking for advice
from this group.

You'll find an answer to the second part of your question below.

On Thu, Jul 23, 2009 at 6:11 PM, ZZzhu0...@gmail.com wrote:

 Hi,

 I'm trying to do some copy number analysis of SNP6 data with
 aroma.affymetrix package.  I followed the instructions for cRMA v2
 (followed by CBS segmentation).  The codes ran smoothly except for the
 occasional appearance of the following message: simpleError in if
 (regexpr(pattern, header$identifier) == -1) { throw(Rcache file
 format error (', pathname, '). Invalid identifier: , header
 $identifier)}: argument is of length zero

 However, the resulting regions.xls file look rather
 strange as it essentially contains the entire genome instead of a list
 of regions with CN change.  Am I missing something here?  Your advice
 will be greatly appreciated!


The output you have pasted is a list of all regions between CN
breakpoints (and their associated mean signal value) as detected by
CBS on chromosome 1 in your sample. 23 breakpoints have been detected
by CBS, hence 24 regions are reported. This is the output of a
segmentation algorithm, not a calling algorithm, so it does not claim
that some regions are normal and other have CN changes.

You can see what the results look like using the ChromosomeExplorer by calling

display(ce)

This type of output is not specific to CBS: you would obtain the same
type of output (but not exactly the same regions) if you had used GLAD
or HaarSeg for the segmentation (using GladModel or HaarSegModel
instead of CbsModel).

Hope this helps,

Pierre.

 Thank you so much,

 ZZ

 results from regions.xls file (for chromosome 1 and one of the
 samples):

 chromosome      start   stop    mean
 1       51599   16024215   0.044
 1       16026085        16026513         -1.597
 1       16026789        65603493         0.028
 1       65604012        101989769        -0.028
 1       101992806 107546773     -0.089
 1       107551303        108227165      -0.035
 1       108227977        72261      0.02
 1       75616        85496      -0.215
 1       89708        117478252      0.019
 1       117480483        146842186      -0.01
 1       146851962        147523316      -0.242
 1       147526041        152059582      -0.004
 1       152062361        155683396      0.036
 1       155687575        167483561      -0.014
 1       167500599        167505369      -1.075
 1       167508391        171552881      -0.039
 1       171555366        184106698      -0.005
 1       184107922        198087432      -0.089
 1       198087435        221395875      -0.007
 1       221395906        223280177      0.018
 1       223283888        223459246      -0.103
 1       223459312        227877793      0.022
 1       227883480        227886820      -2.806
 1       227887054        247191012      0.001

 library(aroma.affymetrix)
 log - Arguments$getVerbose(-8, timestamp=TRUE)
 cdf - AffymetrixCdfFile$byChipType(GenomeWideSNP_6, tags=Full)
 csR - AffymetrixCelSet$byName(testSet, cdf=cdf)
 acc - AllelicCrosstalkCalibration(csR, model=CRMAv2)
 csC - process(acc, verbose=log)
 bpn - BasePositionNormalization(csC, target=zero)
 csN - process(bpn, verbose=log)
 plm - AvgCnPlm(csN, mergeStrands=TRUE, combineAlleles=TRUE)
 fitCnProbes(plm, verbose=log)
 fit(plm, verbose=log)
 ces - getChipEffectSet(plm)
 fln - FragmentLengthNormalization(ces, target=zero)
 cesN - process(fln, verbose=log)
 cbs - CbsModel(cesN)
 ce - ChromosomeExplorer(cbs)
 process(ce,chromosomes=c(1),verbose=log)

 sessionInfo()
 R version 2.9.1 (2009-06-26)
 x86_64-unknown-linux-gnu

 locale:
 LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

 attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base

 other attached packages:
  [1] aroma.affymetrix_1.1.1 aroma.apd_0.1.6        affxparser_1.16.0
  [4] R.huge_0.1.8           aroma.core_1.1.2       aroma.light_1.12.2
  [7] matrixStats_0.1.6      R.rsp_0.3.4            R.filesets_0.5.2
 [10] digest_0.3.1           R.cache_0.1.7          R.utils_1.1.7
 [13] R.oo_1.4.8             R.methodsS3_1.0.3




 


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[aroma.affymetrix] Re: defining cell files

[Pierre Neuvial]

Hi Myriam,

On Thu, Jun 4, 2009 at 4:38 AM, Myriam myriam.peyr...@ki.se wrote:

 Hi,

 I have done (and seems OK, no error message) the low level analysis of
 the GenomeWideSNP_6.0 for preparing the analysis of my Affymetrix
 results in 50 samples.
 However, I cannot get through the steps of defining the CEL files set.
 I have put all the CEL files in rawData/CLP/GenomeWideSNP_6.0 folder.
 How should I define the set of CEL files to be analysed and which are
 contained in that subfolder?
 Tried command:
  cs - AffymetrixCelSet$byName(CLP, cdf=cdf)
 but error: AffymetrixCelSet not found

The name of the folder containing the CEL files should match the name
of the chip type exactly. In your case it should be

rawData/CLP/GenomeWideSNP_6.0

not

rawData/CLP/GenomeWideSNP_6

Does this work now ?

For future posts: it's better to give the complete R output; In your
case aroma.affymetrix probably reports something like:

Cannot create AffymetrixCelSet.  *No such directory: CLP/GenomeWideSNP_6*

which tells you (and us) where the problem comes from.

Best,

Pierre


 I am a bit lost, as a beginner. Sorry to bother but hopefully one of
 you can help me?

 Thanks in advance,
 Myriam

 


--~--~-~--~~~---~--~~
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traceback(), and 3) to post a complete code example.


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[aroma.affymetrix] Re: accessing CnChipEffectSet

[Pierre Neuvial]

Hi Michael,

On Tue, May 5, 2009 at 2:01 PM, mbaudis mbau...@gmail.com wrote:

 Dear all,

 when plotting local copy number values after normalization/chip
 effects etc., one has to load the CnChipEffectSet (e.g.:

 cdf - getCdf(cesN)
 gi - getGenomeInformation(cdf)

 Is there a shortcut to load the cesN object, besides running an
 analysis script? although this wouldn't take too long, if one has kept
 the whole file structure after analysis, it is way too much for CGIs
 etc. Is there a shortcut I am not aware of?


Try using CnChipEffectSet$byName. For example if you wish to work with
the total copy number data generated here :

http://groups.google.com/group/aroma-affymetrix/web/estimation-of-total-copy-numbers-using-the-crma-v2-method

you can do:

verbose - Arguments$getVerbose(-8, timestamp=TRUE)

chipType - GenomeWideSNP_6
dataset - HapMap270,6.0,CEU,testSet;
tags - ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY;

cesN - CnChipEffectSet$byName(dataset, tags=tags, chipType=chipType,
mergeStrands=TRUE, combineAlleles=TRUE, verbose=log);

of course the tags and other options have to be adapted to the
analysis you did in the first place.

Hope this helps,

Pierre.

 Thanks,

 Michael.
 


--~--~-~--~~~---~--~~
When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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[aroma.affymetrix] Re: little mistake at estimation-of-total-copy-numbers-using-the-crma-v2-method page?

[Pierre Neuvial]

Hi,

Thanks, that's fixed now.

Pierre.


On Sat, Apr 25, 2009 at 4:56 AM, mako ma.ko...@gmail.com wrote:

 Hi, Henrik and members

 At first, congratulations on 3 years anniversary!

 I may find little mistake at following URL.
 http://groups.google.com/group/aroma-affymetrix/web/estimation-of-total-copy-numbers-using-the-crma-v2-method

  start paste
 Step 3 - Probe summarization
 (snip..)
 Here we choose to fit allele-specific CN estimates, because we can
 always get total CN signals downstreams.
 plm - AvgCnPlm(csN, mergeStrands=TRUE, combineAlleles=TRUE)
  end paste

 I think Here we choose to fit allele-specific CN estimates is
 incorrect. It seems that  Here we choose to fit total CN signals
 estimate.
 if so, I would be grateful if you could correct it.

 --
 Kohda Masakazu

 Research Center for Genomic Medicine
 Saitama Medical University
 


--~--~-~--~~~---~--~~
When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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[aroma.affymetrix] Re: to use an array list file

[Pierre Neuvial]

Hi,

On Thu, Feb 12, 2009 at 4:25 PM, wukong wukongsu...@gmail.com wrote:

 I am wondering whether aroma-affymetrix can read in CEL files that are
 scattered in several directories.
 For example, the user may want to provide a text file specifying the
 full paths of CEL files.
 The reason is that I want to process these CEL files together, however
 I don't want to copy them to one folder.

Assuming that dataset1 and dataset2 are the names of two data sets you
want to combine, that correspond to the same chip type, you can do

cdf - AffymetrixCdfFile$byChipType(chipType, tags=Full)

csR1 - AffymetrixCelSet$byName(dataset1, cdf=cdf)
csR2 - AffymetrixCelSet$byName(dataset2, cdf=cdf)

csR - append(csR1, csR2)

Note that 'csR' will inherit the name of 'csR1'. To override this, do

setFullName(csR, Combined,tag1,tag2)
print(csR)

Then you can work with this combined csR as you would do for any data set.

Note: Depending on the type of analysis you want to do, processing all
CEL files together or individually, or by batches can lead to the same
exact results: that's the power of single array methods (now it sounds
like it's Henrik speaking...). This is the case for the CRMAv2 method
for analyzing GenomeWide SNP chips.

Thus, if a single array method is available to analyse your chip type,
you might want to analyze the CEL files in each directory separately,
and then combine the resulting 'ChipEffectSet', again using the
'append' method. This is discussed in the following thread:

http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/b7d025724ff2deb5

This can be really useful if you want to analyze large number of chips.

Hope this helps,

Pierre.


 Thanks.

 


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[aroma.affymetrix] Re: use a few normal samples as the reference set

[Pierre Neuvial]

Hi,

I guess that if cesN is your chip-effect set (containing all 8
arrays), and if 1:4 are the normal samples you want to do

cesNN - extract(cesN, 1:4)
ceR - getAverageFile(cesNN, verbose=verbose)

and then use this reference as you did before. Does this help ?

Cheers,

Pierre.


On Tue, Jan 27, 2009 at 8:14 AM, Qicheng Ma qicheng...@gmail.com wrote:
 Hi Henrik,

   For each location, the raw CN is calculated as the chip effect
 relative to the chip effect of a normal reference sample.  If no reference
 sample is available, a robust average across all samples can be used
 instead.

Current documentation shows how to use the whole dataset (including
 the test sample) as the reference sample. Could you please tell me how to
 use a small number of normal samples as the reference sample, instead of the
 all the samples, which include the test sample, as the reference sample,
 e.g., we have 8 tumor samples, 4 normal samples, how to use the 4 normal
 samples as the reference sample.

 Thanks,

 Qicheng

 


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[aroma.affymetrix] Wrong layout in plotAllelePairs

[Pierre Neuvial]

Hi,

I have followed the steps of the CRMAv2 vignette:

http://groups.google.com/group/aroma-affymetrix/web/estimation-of-total-copy-numbers-using-the-crma-v2-method

using aroma.affymetrix version 1.0.0 and I got the following warning:

 plotAllelePairs(acc, array=array, what=input, xlim=xlim/3)
Warning message:
In matrix(seq(length = nbrOfPairs), nrow = floor(sqrt(nbrOfPairs))) :
  data length [7] is not a sub-multiple or multiple of the number of rows [2]

This is because there are now *7* allele probe pair groups, not 6:

 names(getSetsOfProbes(acc)$snp)
[1] A/C A/G A/T C/G C/T G/T missing

As a result the plot layout is wrong:

 nbrOfPairs - length(getSetsOfProbes(acc)$snp)
 matrix(seq(length = nbrOfPairs), nrow = floor(sqrt(nbrOfPairs)))
 [,1] [,2] [,3] [,4]
[1,]1357
[2,]2461
Warning message:
In matrix(seq(length = nbrOfPairs), nrow = floor(sqrt(nbrOfPairs))) :
  data length [7] is not a sub-multiple or multiple of the number of rows [2]

Maybe the easiest fix is to plot only the non missing allele pairs.

Note that if one wants to use several central nucleotides instead of one, as in

alpha - c(0.1, 0.075, 0.05, 0.03, 0.01, 0.0025, 1e-3, 1e-4);
acc - AllelicCrosstalkCalibration(csR, alpha=alpha, pairBy=sequence, B=3)

the number of allele pairs grows quickly: in this particular case
there are 96 allele pairs + 1 missing.
So maybe we it would make sense to hardcode a not to complex layout,
e. g. layout(matrix(seq(length=6, nrow=2))) ?

Cheers,

Pierre

 sessionInfo()
R version 2.8.1 (2008-12-22)
i386-apple-darwin8.11.1

locale:
C

attached base packages:
[1] stats graphics  grDevices datasets  utils methods   base

other attached packages:
 [1] sfit_0.1.5 aroma.affymetrix_1.0.0 aroma.apd_0.1.3
 [4] R.huge_0.1.6   affxparser_1.14.0  aroma.core_1.0.0
 [7] aroma.light_1.9.2  digest_0.3.1   matrixStats_0.1.3
[10] R.rsp_0.3.4R.cache_0.1.7  R.utils_1.1.3
[13] R.oo_1.4.6 R.methodsS3_1.0.3

--~--~-~--~~~---~--~~
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version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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[aroma.affymetrix] Re: Wrong layout in plotAllelePairs

[Pierre Neuvial]

Hi again,

Henrik pointed to me that plotAllelePairs.AllelicCrosstalkCalibration
has an argument 'pairs' which can be used to specify the indexes of
the pairs that one wants to plot. In my case

plotAllelePairs(acc, array=array, pairs=1:6, what=input, xlim=xlim/3)

does the job.

Cheers,

Pierre


On Wed, Jan 14, 2009 at 11:56 AM, Pierre Neuvial
pie...@stat.berkeley.edu wrote:
 Hi,

 I have followed the steps of the CRMAv2 vignette:

 http://groups.google.com/group/aroma-affymetrix/web/estimation-of-total-copy-numbers-using-the-crma-v2-method

 using aroma.affymetrix version 1.0.0 and I got the following warning:

 plotAllelePairs(acc, array=array, what=input, xlim=xlim/3)
 Warning message:
 In matrix(seq(length = nbrOfPairs), nrow = floor(sqrt(nbrOfPairs))) :
  data length [7] is not a sub-multiple or multiple of the number of rows [2]

 This is because there are now *7* allele probe pair groups, not 6:

 names(getSetsOfProbes(acc)$snp)
 [1] A/C A/G A/T C/G C/T G/T missing

 As a result the plot layout is wrong:

 nbrOfPairs - length(getSetsOfProbes(acc)$snp)
 matrix(seq(length = nbrOfPairs), nrow = floor(sqrt(nbrOfPairs)))
 [,1] [,2] [,3] [,4]
 [1,]1357
 [2,]2461
 Warning message:
 In matrix(seq(length = nbrOfPairs), nrow = floor(sqrt(nbrOfPairs))) :
  data length [7] is not a sub-multiple or multiple of the number of rows [2]

 Maybe the easiest fix is to plot only the non missing allele pairs.

 Note that if one wants to use several central nucleotides instead of one, as 
 in

 alpha - c(0.1, 0.075, 0.05, 0.03, 0.01, 0.0025, 1e-3, 1e-4);
 acc - AllelicCrosstalkCalibration(csR, alpha=alpha, pairBy=sequence, B=3)

 the number of allele pairs grows quickly: in this particular case
 there are 96 allele pairs + 1 missing.
 So maybe we it would make sense to hardcode a not to complex layout,
 e. g. layout(matrix(seq(length=6, nrow=2))) ?

 Cheers,

 Pierre

 sessionInfo()
 R version 2.8.1 (2008-12-22)
 i386-apple-darwin8.11.1

 locale:
 C

 attached base packages:
 [1] stats graphics  grDevices datasets  utils methods   base

 other attached packages:
  [1] sfit_0.1.5 aroma.affymetrix_1.0.0 aroma.apd_0.1.3
  [4] R.huge_0.1.6   affxparser_1.14.0  aroma.core_1.0.0
  [7] aroma.light_1.9.2  digest_0.3.1   matrixStats_0.1.3
 [10] R.rsp_0.3.4R.cache_0.1.7  R.utils_1.1.3
 [13] R.oo_1.4.6 R.methodsS3_1.0.3


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When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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[aroma.affymetrix] Re: AllelicCrosstalkCalibration(..., model=CRMAv2, B=3)

[Pierre Neuvial]

Thanks Henrik, it worked.

Pierre

On Fri, Jan 9, 2009 at 10:14 PM, Henrik Bengtsson h...@stat.berkeley.edu 
wrote:

 Hi.

 On Fri, Jan 9, 2009 at 6:22 PM, Pierre Neuvial pie...@stat.berkeley.edu 
 wrote:

 Hi,

 I would like to perform allelic crosstalk calibration using the 3
 central nucleotides instead of 1, which is the default in CRMAv2. I've
 tried this:

 acc - AllelicCrosstalkCalibration(csR, model=CRMAv2, B=3, tags=B=3)

 The setup is (currently) that if you specify model=CRMAv2, this will
 override all other parameters.  Instead you want to keep the default
 of 'model' (=asis) by leaving it out.  To get the default CRMAv2
 parameters, but B=3, do:

 alpha - c(0.1, 0.075, 0.05, 0.03, 0.01, 0.0025, 1e-3, 1e-4);
 acc - AllelicCrosstalkCalibration(csR, alpha=alpha, pairBy=sequence, B=3)

 Note that when B != 1, you will automatically get an extra B=integer
 tag, e.g. B=3.

 FYI, to *add* an extra tag, you must not forget to keep the other,
 which you specify by an asterisk, e.g. tags=*,myTag or alternatively
 tags=c(*, myTag).

 I'll see if I can find a way to interpret arguments model=CRMAv2,
 B=3, to mean CRMAv2 parameters but with B=3.

 Hope this works

 Henrik


 but parameter B is still 1:

 print(acc)
 AllelicCrosstalkCalibration:
 Data set: HapMap270
 Input tags: 6.0,CEU,testSet
 User tags: B=3
 Asterisk ('*') tags: ACC,ra,-XY
 Output tags: 6.0,CEU,testSet,B=3
 Number of files: 6 (395.13MB)
 Platform: Affymetrix
 Chip type: GenomeWideSNP_6,Full
 Algorithm parameters: (rescaleBy: chr all, targetAvg: num 2200,
 subsetToAvg: chr -XY, mergeShifts: logi TRUE, B: int 1, flavor: chr
 sfit, algorithmParameters:List of 3, ..$ alpha: num [1:8] 0.1 0.075
 0.05 0.03 0.01 0.0025 0.001 0.0001, ..$ q: num 2, ..$ Q: num 98)
 Output path: probeData/HapMap270,6.0,CEU,testSet,B=3/GenomeWideSNP_6
 Is done: FALSE
 RAM: 0.00MB

 I guess that model=CRMAv2 forces B to be 1. Then how can I set up
 another model with B=3 ?

 Thanks,

 Pierre


 library(aroma.affymetrix)
 Loading required package: R.utils
 Loading required package: R.oo
 Loading required package: R.methodsS3
 R.methodsS3 v1.0.3 (2008-07-02) successfully loaded. See ?R.methodsS3 for 
 help.
 R.oo v1.4.6 (2008-08-11) successfully loaded. See ?R.oo for help.
 R.utils v1.1.1 (2008-12-03) successfully loaded. See ?R.utils for help.
 Loading required package: aroma.core
 Loading required package: R.cache
 R.cache v0.1.7 (2008-02-27) successfully loaded. See ?R.cache for help.
 Loading required package: R.rsp
 R.rsp v0.3.4 (2008-03-06) successfully loaded. See ?R.rsp for help.
  Type browseRsp() to open the RSP main menu in your browser.
 Loading required package: matrixStats
 Loading required package: digest
 Loading required package: aroma.light
 aroma.light v1.9.2 (2008-09-10) successfully loaded. See ?aroma.light for 
 help.
 aroma.core v0.9.6 (2008-12-04) successfully loaded. See ?aroma.core for help.
 Loading required package: affxparser
 Loading required package: R.huge
 R.huge v0.1.6 (2008-07-03) successfully loaded. See ?R.huge for help.
 Loading required package: aroma.apd
 aroma.apd v0.1.3 (2006-06-14) successfully loaded. See ?aroma.apd for help.
 aroma.affymetrix v0.9.6.4 (2008-12-17) successfully loaded. See
 ?aroma.affymetrix for help.
 log - verbose - Arguments$getVerbose(-10, timestamp=TRUE)
 options(digits=4)
 cdf - AffymetrixCdfFile$byChipType(GenomeWideSNP_6, tags=Full)
 csR - AffymetrixCelSet$byName(HapMap270,6.0,CEU,testSet, cdf=cdf)
 print(csR)
 AffymetrixCelSet:
 Name: HapMap270
 Tags: 6.0,CEU,testSet
 Path: rawData/HapMap270,6.0,CEU,testSet/GenomeWideSNP_6
 Platform: Affymetrix
 Chip type: GenomeWideSNP_6,Full
 Number of arrays: 6
 Names: NA06985, NA06991, ..., NA07019
 Time period: 2007-03-06 12:13:04 -- 2007-03-06 19:17:16
 Total file size: 395.13MB
 RAM: 0.01MB
 Warning messages:
 1: In rawToChar(raw) :
  truncating string with embedded nul:
 'GenomeWideSNP_6\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
 2: In rawToChar(raw) :
  truncating string with embedded nul:
 'GenomeWideSNP_6\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
 3: In rawToChar(raw) :
  truncating string with embedded nul:
 'GenomeWideSNP_6\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
 4: In rawToChar(raw) :
  truncating string with embedded nul:
 'GenomeWideSNP_6\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
 5: In rawToChar(raw) :
  truncating string with embedded nul:
 'GenomeWideSNP_6\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0

[aroma.affymetrix] AllelicCrosstalkCalibration(..., model=CRMAv2, B=3)

[Pierre Neuvial]

Hi,

I would like to perform allelic crosstalk calibration using the 3
central nucleotides instead of 1, which is the default in CRMAv2. I've
tried this:

 acc - AllelicCrosstalkCalibration(csR, model=CRMAv2, B=3, tags=B=3)

but parameter B is still 1:

 print(acc)
AllelicCrosstalkCalibration:
Data set: HapMap270
Input tags: 6.0,CEU,testSet
User tags: B=3
Asterisk ('*') tags: ACC,ra,-XY
Output tags: 6.0,CEU,testSet,B=3
Number of files: 6 (395.13MB)
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full
Algorithm parameters: (rescaleBy: chr all, targetAvg: num 2200,
subsetToAvg: chr -XY, mergeShifts: logi TRUE, B: int 1, flavor: chr
sfit, algorithmParameters:List of 3, ..$ alpha: num [1:8] 0.1 0.075
0.05 0.03 0.01 0.0025 0.001 0.0001, ..$ q: num 2, ..$ Q: num 98)
Output path: probeData/HapMap270,6.0,CEU,testSet,B=3/GenomeWideSNP_6
Is done: FALSE
RAM: 0.00MB

I guess that model=CRMAv2 forces B to be 1. Then how can I set up
another model with B=3 ?

Thanks,

Pierre


 library(aroma.affymetrix)
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.0.3 (2008-07-02) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.4.6 (2008-08-11) successfully loaded. See ?R.oo for help.
R.utils v1.1.1 (2008-12-03) successfully loaded. See ?R.utils for help.
Loading required package: aroma.core
Loading required package: R.cache
R.cache v0.1.7 (2008-02-27) successfully loaded. See ?R.cache for help.
Loading required package: R.rsp
R.rsp v0.3.4 (2008-03-06) successfully loaded. See ?R.rsp for help.
 Type browseRsp() to open the RSP main menu in your browser.
Loading required package: matrixStats
Loading required package: digest
Loading required package: aroma.light
aroma.light v1.9.2 (2008-09-10) successfully loaded. See ?aroma.light for help.
aroma.core v0.9.6 (2008-12-04) successfully loaded. See ?aroma.core for help.
Loading required package: affxparser
Loading required package: R.huge
R.huge v0.1.6 (2008-07-03) successfully loaded. See ?R.huge for help.
Loading required package: aroma.apd
aroma.apd v0.1.3 (2006-06-14) successfully loaded. See ?aroma.apd for help.
aroma.affymetrix v0.9.6.4 (2008-12-17) successfully loaded. See
?aroma.affymetrix for help.
 log - verbose - Arguments$getVerbose(-10, timestamp=TRUE)
 options(digits=4)
 cdf - AffymetrixCdfFile$byChipType(GenomeWideSNP_6, tags=Full)
 csR - AffymetrixCelSet$byName(HapMap270,6.0,CEU,testSet, cdf=cdf)
 print(csR)
AffymetrixCelSet:
Name: HapMap270
Tags: 6.0,CEU,testSet
Path: rawData/HapMap270,6.0,CEU,testSet/GenomeWideSNP_6
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full
Number of arrays: 6
Names: NA06985, NA06991, ..., NA07019
Time period: 2007-03-06 12:13:04 -- 2007-03-06 19:17:16
Total file size: 395.13MB
RAM: 0.01MB
Warning messages:
1: In rawToChar(raw) :
  truncating string with embedded nul:
'GenomeWideSNP_6\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
2: In rawToChar(raw) :
  truncating string with embedded nul:
'GenomeWideSNP_6\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
3: In rawToChar(raw) :
  truncating string with embedded nul:
'GenomeWideSNP_6\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
4: In rawToChar(raw) :
  truncating string with embedded nul:
'GenomeWideSNP_6\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
5: In rawToChar(raw) :
  truncating string with embedded nul:
'GenomeWideSNP_6\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
6: In rawToChar(raw) :
  truncating string with embedded nul:
'GenomeWideSNP_6\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
 acc - AllelicCrosstalkCalibration(csR, model=CRMAv2, B=3, tags=B=3)
 print(acc)
AllelicCrosstalkCalibration:
Data set: HapMap270
Input tags: 6.0,CEU,testSet
User tags: B=3
Asterisk ('*') tags: ACC,ra,-XY
Output tags: 6.0,CEU,testSet,B=3
Number of files: 6 (395.13MB)
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full
Algorithm parameters: (rescaleBy: chr all, targetAvg: num 2200,
subsetToAvg: chr -XY, mergeShifts: logi TRUE, B: int 1, flavor: chr
sfit, algorithmParameters:List of 3, ..$ alpha: num [1:8] 0.1 0.075
0.05 0.03 0.01 0.0025 0.001 0.0001, ..$ q: num 2, ..$ Q: num 98)
Output path: probeData/HapMap270,6.0,CEU,testSet,B=3/GenomeWideSNP_6
Is done: FALSE
RAM: 0.00MB
 sessionInfo()
R 

[aroma.affymetrix] Re: Error in fragment length normalization

[Pierre Neuvial]

Hello Mike,

I'm not sure what your problem is but it would certainly be helpful if
you could post a complete code example, the corresponding output, and
your sessionInfo().

That said, there have been several posts on the list about related
problems, see e.g this one:

http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/ccb58ee61f3f3aa/b8b552a10135c2b3?lnk=gstq=cannot+fit+enzyme+to+target+function#b8b552a10135c2b3

Have you checked them ? Do they help ?

Pierre

On Tue, Jan 6, 2009 at 8:18 PM, Mike B michael.buck...@csiro.au wrote:

 In calling process.FragmentLengthNormalization() I am getting the
 exception ...

 Exception: Cannot fit target function to enzyme, because there are no
 (finite) data points that are unique to this enzyme: 1

 I am using 90 samples in the 50K Xba240 chip.

 What is the problem? I have run this successfully on a different
 experiment with 20 CEL files. Is there a workaround?

   Mike

 


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