[aroma.affymetrix] Re: Could not loacate CystoScanHD_Array annotation

[Chengyu Liu]

Addtional information. 
The file structure is like this,
├── annotationData
│   └── chipTypes
│   └── CytoScanHD_Array
│   ├── CytoScanHD_Array.cdf
│   └── NetAffx
│   └── CytoScanHD_Array_annot.csv
└── rawData
└── dataset1
└── CytoScanHD_Array
├── 010213-01-NB_(CytoScanHD_Array).CEL
└── 010213-01-TB_(CytoScanHD_Array).CEL



On Monday, December 15, 2014 3:51:46 PM UTC+2, Chengyu Liu wrote:

 Hi,

 I am trying to read annotation file of CytoScanHD_Array, but somehow it 
 could not locate it.

 I followed the tutorial in the web 
 http://aroma-project.org/setup/annotationData/. I am using NetAffx 
 Annotation Files (I could not find CDF file) .
 I created folder annotationData/chipTypes/CytoScanHD_Array/NetAffx/  and 
 put annotation file CytoScanHD_Array_annot.csv there.

 I ran AffymetrixNetAffxCsvFile$byChipType(CytoScanHD_Array) at parent 
 directory of annotationData.

 It gave error Error in grep(pattern, basename(files0)) : invalid 
 'pattern' argument

 Does anyone know what was wrong ?

 Br,
 C.Y


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Re: [aroma.affymetrix] Could not loacate CystoScanHD_Array annotation

[Chengyu Liu]

Thanks.

I tried to bypass the NetAffx issue. I downloaded the cdf file from aroma 
(http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/) 
and Affymetrix website.
Annotation file can be located, but following functions does not work. It 
was my first time to deal with aroma.afymetrix package. Maybe I was using 
wrong way.

Any comments are appreciated. 

 cdf - AffymetrixCdfFile$byChipType('CytoScanHD_Array');
 print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/CytoScanHD_Array
Filename: CytoScanHD_Array.cdf
File size: 612.27 MB (642007896 bytes)
Chip type: CytoScanHD_Array
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 2822125
Cells per unit: 2.44
Number of QC units: 4

gi - getGenomeInformation(cdf)
[2014-12-15 18:28:32] Exception: Failed to retrieve genome information for 
this chip type: CytoScanHD_Array

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

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

Error: Failed to retrieve genome information for this chip type: 
CytoScanHD_Array

si - getSnpInformation(cdf)
20141215 18:31:41|Defining DChipSnpInformation from chip type...
20141215 18:31:41| Chip type: CytoScanHD_Array
20141215 18:31:41| Version:
20141215 18:31:41| Located pathname:
20141215 18:31:41|Defining DChipSnpInformation from chip type...done
[2014-12-15 18:31:41] Exception: Failed to retrieve SNP information for 
this chip type: CytoScanHD_Array
 
  at #02. getSnpInformation.AffymetrixCdfFile(cdf)
  - getSnpInformation.AffymetrixCdfFile() is in environment 
'aroma.affymetrix'
 
  at #01. getSnpInformation(cdf)
  - getSnpInformation() is in environment 'aroma.affymetrix'
 
Error: Failed to retrieve SNP information for this chip type: 
CytoScanHD_Array

acs - AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
[2014-12-15 18:31:50] Exception: Failed to create AromaCellSequenceFile 
object. Could not locate an annotation data file for chip type 
'CytoScanHD_Array' (without requiring any tags) and with filename extension 
'acs'.

  at #03. byChipType.AromaMicroarrayTabularBinaryFile(static, ...)
  - byChipType.AromaMicroarrayTabularBinaryFile() is in environment 
'aroma.core'

  at #02. byChipType(static, ...)
  - byChipType() is in environment 'aroma.core'
  - originating from 'text'

  at #01. AromaCellSequenceFile$byChipType(getChipType(cdf, fullname = 
FALSE))
  - AromaCellSequenceFile$byChipType() is local of the calling 
function

Error: Failed to create AromaCellSequenceFile object. Could not locate an 
annotation data file for chip type 'CytoScanHD_Array' (without requiring 
any tags) and with filename extension 'acs'.


On Monday, December 15, 2014 6:27:51 PM UTC+2, Henrik Bengtsson wrote:

 I can reproduce this; 

  csv - AffymetrixNetAffxCsvFile$byChipType(chipType) 
 Error in grep(pattern, basename(files0)) : invalid 'pattern' argument 

 I'll investigate. 

 /Henrik 

 On Mon, Dec 15, 2014 at 5:51 AM, Chengyu Liu chengyu...@gmail.com 
 javascript: wrote: 
  Hi, 
  
  I am trying to read annotation file of CytoScanHD_Array, but somehow it 
  could not locate it. 
  
  I followed the tutorial in the web 
  http://aroma-project.org/setup/annotationData/. I am using NetAffx 
  Annotation Files (I could not find CDF file) . 
  I created folder annotationData/chipTypes/CytoScanHD_Array/NetAffx/  and 
 put 
  annotation file CytoScanHD_Array_annot.csv there. 
  
  I ran AffymetrixNetAffxCsvFile$byChipType(CytoScanHD_Array) at parent 
  directory of annotationData. 
  
  It gave error Error in grep(pattern, basename(files0)) : invalid 
 'pattern' 
  argument 
  
  Does anyone know what was wrong ? 
  
  Br, 
  C.Y 
  
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Re: [aroma.affymetrix] Encountered ERROR while extracting chip effects

[Henrik Bengtsson]

On Thu, Dec 11, 2014 at 4:52 AM, Rishi Das Roy rishi.das...@gmail.com wrote:
 Hi

 Thanks for your reply. I can understand that I can identify alternative
 splicing through FIRMA more confidently. However I also want to identify
 differentially expressed genes. I have not find any documentation regarding
 this in aroma-project.org .

 Please provide any example to find DE genes through  aroma.affymetrix.

If you look at http://aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis,
you find the following passages:

There are two options, regardless of the kind of custom CDF you use.
To fit a summary of the entire transcript (i.e. estimate the overall
expression for the transcript), do:

plmTr - ExonRmaPlm(csN, mergeGroups=TRUE)
print(plmTr)

and then a bit later also:

To extract the estimates (transcript or probeset) use either
extractMatrix() or extractDataFrame() on the ChipEffectSet that
corresponds to the plm object:

cesTr - getChipEffectSet(plmTr)
trFit - extractDataFrame(cesTr, units=1:3, addNames=TRUE)

This will give a data.frame with three rows, each row corresponding to
a unit/transcript.

Hope this helps

Henrik


 Thanks
 rishi



 On Wednesday, December 10, 2014 11:39:50 PM UTC+2, Henrik Bengtsson wrote:

 Hi,

 you cannot use RMA on exon-arrays, you will need to use exon-aware
 method such as FIRMA (e.g.
 http://aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis).

 Hope this helps

 Henrik

 PS. For http://aroma-project.org/replication/RMA, I've updated it to
 use `theta - extractTheta(ces)` instead of `theta -
 extractMatrix(ces)`.  This will allow you to set the row names.  But
 as you'll find out, 'theta' becomes an JxKxI array for exon-arrays,
 where J is the number of genes, I is the number of samples and K is
 the maximum number of exons per gene found.  In other words, using
 doRMA() on exon arrays gives you at best exon-specific estimates (and
 they are not very good estimates - FIRMA is doing a much better job on
 that).



 On Wed, Dec 10, 2014 at 1:51 AM, Rishi Das Roy rishi@gmail.com
 wrote:
  Hi,
 
  I was trying to perform RMA on Mouse Exon 1.0 ST Array as described in
  aroma
  website (link) using custom cdf
  MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf.gz .
 
  I have executed following code in R
 
  cdf - AffymetrixCdfFile$byChipType(chipType,
  tags=coreR1,A20080718,MR)
  cs - AffymetrixCelSet$byName(data_CEL, cdf=cdf);
  bc - RmaBackgroundCorrection(cs);
  csB - process(bc);
  qn - QuantileNormalization(csB, typesToUpdate=pm);
  csN - process(qn);
  plm - RmaPlm(csN);
  fit(plm);
  ces - getChipEffectSet(plm);
  theta - extractMatrix(ces);
  rownames(theta) - getUnitNames(cdf);
  Error in `rownames-`(`*tmp*`, value = c(6838637, 6992377,
  6901592,  :
length of 'dimnames' [1] not equal to array extent
 
  Please help me to understand this error and how can I solve this. The
  session info is given below.
 
  With regards
  Rishi
 
  R version 3.1.2 (2014-10-31)
  Platform: x86_64-pc-linux-gnu (64-bit)
 
  locale:
   [1] LC_CTYPE=fi_FI.UTF-8LC_NUMERIC=CLC_TIME=en_GB
  LC_COLLATE=en_GBLC_MONETARY=fi_FI.UTF-8
   [6] LC_MESSAGES=en_GB   LC_PAPER=en_GB  LC_NAME=C
  LC_ADDRESS=CLC_TELEPHONE=C
  [11] LC_MEASUREMENT=en_GBLC_IDENTIFICATION=C
 
  attached base packages:
  [1] stats4parallel  stats graphics  grDevices utils datasets
  methods   base
 
  other attached packages:
   [1] preprocessCore_1.28.0 aroma.light_2.2.0
  aroma.affymetrix_2.12.8   aroma.core_2.12.8
   [5] R.devices_2.12.0  R.filesets_2.6.0
  R.utils_1.34.0R.oo_1.18.2
   [9] R.methodsS3_1.6.2 affxparser_1.38.0
  pd.moex10st.mm.aceviewg_0.0.1 affy_1.44.0
  [13] BiocInstaller_1.16.1  pd.moex.1.0.st.v1_3.10.0
  RSQLite_1.0.0 DBI_0.3.1
  [17] moex10stmmrefseqcdf_19.0.0AnnotationDbi_1.28.1
  GenomeInfoDb_1.2.3oligo_1.30.0
  [21] Biostrings_2.34.0 XVector_0.6.0
  IRanges_2.0.0 S4Vectors_0.4.0
  [25] Biobase_2.26.0oligoClasses_1.28.0
  BiocGenerics_0.12.1
 
  loaded via a namespace (and not attached):
   [1] affyio_1.34.0aroma.apd_0.5.0  base64enc_0.1-2
  bit_1.1-12   codetools_0.2-8  digest_0.6.5
   [7] DNAcopy_1.40.0   ff_2.2-13foreach_1.4.2
  GenomicRanges_1.18.3 iterators_1.0.7  matrixStats_0.12.2
  [13] PSCBS_0.43.0 R.cache_0.11.0   R.huge_0.8.0
  R.rsp_0.19.6 splines_3.1.2tools_3.1.2
  [19] zlibbioc_1.12.0
 
  --
  --
  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