from:"Hooiveld, Guido"

RE: [aroma.affymetrix] AffymetrixCdfFile$byChipType -- Argument 'nbrOfUnits' contains 1 NA value(s)

2017-04-05 Thread Hooiveld, Guido

Hi,
Creating the CDF object using the same binary CDF file works fine in my hands… 
?? See below.

It has been a while since I extensively used aroma.affymetrix, but I noticed 
the main difference between your and my code is that you specifically set in R 
all relevant directories (cel.directory, annotation.data, etc), whereas I just 
set the working directory (to “aroma.affy.test”). That was the only directory I 
set/specified.

Before starting R/aroma.affymetrix  I downloaded the binary CDF file, and 
within this (working) directory I created the relevant CDF directory (i.e. 
D:\aroma.affy.test\annotationData\chipTypes\RaGene-2_1-st), and then copied the 
CDF into that dir.
Next I ran the code below.

Note that I am on a Windows machine. Also note that since I don’t have some 
RaGene 2.1 CEL files I could not test whether the subsequent normalization goes 
fine.

HTH,
Guido

> setwd("D:\\aroma.affy.test")
>
> library(aroma.affymetrix)
> chipType <- "RaGene-2_1-st"
> cdf <- AffymetrixCdfFile$byChipType(chipType, tags=c("byTranscript-fsetid", 
> "pd.ragene.2.1.st"))
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/RaGene-2_1-st
Filename: RaGene-2_1-st,byTranscript-fsetid,pd.ragene.2.1.st.cdf
File size: 15.00 MiB (15728222 bytes)
Chip type: RaGene-2_1-st,byTranscript-fsetid,pd.ragene.2.1.st
File format: v4 (binary; XDA)
Dimension: 1190x1190
Number of cells: 1416100
Number of units: 36685
Cells per unit: 38.60
Number of QC units: 0
>
>

> sessionInfo()
R version 3.3.1 Patched (2016-10-18 r71535)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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.light_3.4.0  aroma.affymetrix_3.1.0 affxparser_1.46.0  
aroma.core_3.1.0
[5] R.devices_2.15.1   R.filesets_2.11.0  R.utils_2.5.0  
R.oo_1.21.0
[9] R.methodsS3_1.7.1

loaded via a namespace (and not attached):
[1] matrixStats_0.52.0 codetools_0.2-15   listenv_0.6.0  future_1.4.0   
digest_0.6.12
 [6] R.huge_0.9.0   PSCBS_0.62.0   tools_3.3.1R.cache_0.12.0
 parallel_3.3.1
[11] base64enc_0.1-3aroma.apd_0.6.0R.rsp_0.40.0   globals_0.9.0 
 DNAcopy_1.48.0
>

-
Guido Hooiveld, PhD
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition & Health
Wageningen University
Visiting address:   Mail address:
HELIX (Building 124), room 2048
Stippeneng 4   PO Box 17
6708 WE Wageningen  6700 AA Wageningen
the Netherlands   the Netherlands

tel: (+) 31 317 485788
fax: (+) 31 317 483342
email:  guido.hooiv...@wur.nl
internet:   http://www.wur.nl/nmg/hooiveld
internet:   http://www.wur.nl/nmg
http://scholar.google.com/citations?user=qFHaMnoJ
http://www.researcherid.com/rid/F-4912-2010

From: aroma-affymetrix@googlegroups.com 
[mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Sophie Marion de Procé
Sent: Monday, April 03, 2017 18:15
To: aroma.affymetrix 
Subject: [aroma.affymetrix] AffymetrixCdfFile$byChipType -- Argument 
'nbrOfUnits' contains 1 NA value(s)

Dear all,

I'm new to aroma.affymetrix and I seem to be stuck at the cdf file step using 
AffymetrixCdfFile$byChipType.
I've set up the folders and files as advised, and got the cdf file for 
RaGene-2_1-st from http://nmg-r.bioinformatics.nl/NuGO_R.html.
My command to create the cdf object fails with the error (detailed below): 
Argument 'nbrOfUnits' contains 1 NA value(s).

Would you have any suggestion of what I'm doing wrong?

Thanks very much for your help,
Best wishes,
Sophie.


Here is my code:
require(aroma.affymetrix)
require(biomaRt)
require(GenomeGraphs)

wd <- 
"/Users/sdeproce/Documents/AITMAN_GROUP/KO_SHR_rat_strains/Transcriptomes/aroma_affymetrix_wd"
ds <- "myDataSet"
cel.directory <- 
"/Users/sdeproce/Documents/AITMAN_GROUP/KO_SHR_rat_strains/Transcriptomes/aroma_affymetrix_wd/rawData/myDataSet/RaGene-2_1-st"
annotation.data<-"/Users/sdeproce/Documents/AITMAN_GROUP/KO_SHR_rat_strains/Transcriptomes/aroma_affymetrix_wd/annotationData/chipTypes/RaGene-2_1-st"
output.folder <- 
"/Users/sdeproce/Documents/AITMAN_GROUP/KO_SHR_rat_strains/Transcriptomes/aroma_affymetrix_wd/output"
library.file 
<-"/Users/sdeproce/Documents/AITMAN_GROUP/KO_SHR_rat_strains/Transcriptomes/aroma_affymetrix_wd/annotationData/chipTypes/RaGene-2_1-st/RaGene-2_1-st,byTranscript-fsetid,pd.ragene.2.1.st.cdf"
chipType<-"RaGene-2_1-st"
sample.info <-read.table(file=paste(cel.directory,"SampleInformation.txt", 
sep="/"),sep="\t", header=TRUE)

transcript.clusters.NetAffx.36 <- 
read.csv(file=paste(annotation.data,"RaGene-2_1-st-v1.na3

RE: [aroma.affymetrix] Construct cdf file from pgf, clf and gene mapping file

2014-01-23 Thread Hooiveld, Guido

Hi,
I was a little curious to know what these scripts are able to 
construct/convert, so I had a quick look at the codes.
@ Elizabeth (or others):
Although I am not planning to use these (yet), there is one thing that 
(naively?) did not become immediately clear to me: what is the expected content 
of the file "annotExonBoundaries" that is required for the (1st) function 
"annotateProbesets.R", (and how would generate such file)?

>From the description in the script:
exonBoundariesFile=file name of deliminated file with the exon boundaries that 
you want to map the probesets to.
##annotExonBoundaries<-file.path(outdir,"exonBoundaries_proteinCoding_20080819.txt")

Thanks,
Guido

- 
Guido Hooiveld, PhD 
Nutrition, Metabolism & Genomics Group 
Division of Human Nutrition 
Wageningen University 
Biotechnion, Bomenweg 2 
NL-6703 HD Wageningen 
the Netherlands 
tel: (+)31 317 485788 
fax: (+)31 317 483342 
email:  guido.hooiv...@wur.nl
internet:   http://nutrigene.4t.com 
http://scholar.google.com/citations?user=qFHaMnoJ
http://www.researcherid.com/rid/F-4912-2010


-Original Message-
From: aroma-affymetrix@googlegroups.com 
[mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Henrik Bengtsson
Sent: Wednesday, January 22, 2014 21:15
To: aroma-affymetrix@googlegroups.com
Subject: Re: [aroma.affymetrix] Construct cdf file from pgf, clf and gene 
mapping file

Alright, so Elizabeth Purdom found the missing files and kindly sent them to 
me.  I've now uploaded them the http://aroma-project.org server and updated the 
links on http://aroma-project.org/node/40 accordingly.

Hope this helps

Henrik

On Tue, Jan 21, 2014 at 3:35 PM, Henrik Bengtsson 
 wrote:
> Hi,
>
> thanks for reporting on this.
>
> On Mon, Jan 20, 2014 at 2:09 PM, Guilherme Rocha  wrote:
>> Dear all,
>>
>> Does anybody know of any good tools for constructing a cdf file from 
>> affy pgf and clf files?
>>
>> It appears that such tools exist:  
>> http://www.aroma-project.org/node/40
>>
>> The problem is the following 3 links in above address are broken:
>>
>> 1)http://bcgc.lbl.gov/cdfFiles/flat2Cdf.R
>> Flat2cdf.R (constructs a cdf file from a "flat file")
>
> It turns out that that file is the same as
>
> http://bioinf.wehi.edu.au/folders/mrobinson/exon/flat2Cdf.R
>
> I've update the webpage to link to that instead (for now).
>
>>
>> 2)http://bcgc.lbl.gov/cdfFiles/combineProbeInfo.pl
>> combineProbeInfo.pl (combines pgf and clf files into single flat file 
>> with each row containing most of the information needed for each 
>> probe)
>
> Unfortunately, I cannot locate this elsewhere.
>
>>
>> 3)http://bcgc.lbl.gov/cdfFiles/addGeneId.pl
>> addGeneId.pl (takes output of previous pl script and merge it with 
>> probeset-gene map to generate flat file needed by flat2cdf)
>
> Unfortunately, same for this one (and the other links on that page).
>
> If you can generate a "flat" text-files as on illustrated on that 
> page, you could still create a CDF.  However, note that the flat2Cdf() 
> function is rather specific to gene-exon chip types, so if you're 
> looking to create other types of CDF files, it won't work (at least 
> not out of the box).
>
> I've updated http://aroma-project.org/node/40 with the following note:
>
> Note: Several of the links to the external third party R and Perl 
> scripts are broken, i.e. annotateProbesets.R, 
> convertProbesetCSV_differentInput.pl, selectProbes.pl 
> combineProbeInfo.pl, addGeneId.pl.  If you have any of these files 
> sitting around, please consider sending them to use.  Thanks /HB
> 2014-01-20
>
> Thanks,
>
> Henrik
>
>>
>> Any help greatly appreciated.
>>
>> Thanks,
>>
>> Guilherme Rocha
>>
>>
>> --
>> --
>> 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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>> go to http://www.aroma-project.org/forum/
>>
>> ---
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version of the package, 2) to report the output of sessionInfo() and 
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RE: [aroma.affymetrix] gene-centric CDF for HT HG U133A arrays (TCGA GBM data)

2014-01-06 Thread Hooiveld, Guido

Hi,
Did you check the website of the MBNI folks?
AFAIK Manhong Dai et al offer remapped (custom) CDFs for this array type (and 
many others) in various flavors (e.g. based on ENSEMBL gene/transcript, NCBI 
Entrez Gene / RefSeq, etc.)
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp#v17

HTH,
Guido

-
Guido Hooiveld, PhD
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
Wageningen University
Biotechnion, Bomenweg 2
NL-6703 HD Wageningen
the Netherlands
tel: (+)31 317 485788
fax: (+)31 317 483342
email:  guido.hooiv...@wur.nl
internet:   http://nutrigene.4t.com
http://scholar.google.com/citations?user=qFHaMnoJ
http://www.researcherid.com/rid/F-4912-2010

From: aroma-affymetrix@googlegroups.com 
[mailto:aroma-affymetrix@googlegroups.com] On Behalf Of BJ Chen
Sent: Friday, January 03, 2014 23:48
To: aroma-affymetrix@googlegroups.com
Subject: [aroma.affymetrix] gene-centric CDF for HT HG U133A arrays (TCGA GBM 
data)


Hi,

I am wondering if anyone can point me to somewhere I can download the 
gene-centric CDF for HT-HG-U133A arrays. I have searched around, but the only 
CDF I can find is from affymetrix website. I would like to process some arrays 
to get gene-level data. I followed the script example 
(http://www.aroma-project.org/vignettes/GeneSTArrayAnalysis) to extract the 
data, but the data is still at probe level. I appreciate anyone's help.

Thanks,
BJ
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RE: [aroma.affymetrix] CDF file for Human Gene 1.1 st array

2013-11-02 Thread Hooiveld, Guido

Hi Jerry,

Let me first say this: it is impossible for me/Philip to track the problem down 
since we don't have any experience with the analysis of Affymetrix arrays using 
Matlab. We standardly use R/BioC/aroma.affymetrix.
However, I noticed you try to perform gcrma normalization. Since the ST arrays 
consist of PM probes only, GCRMA normalization won't work. What happens if you 
try to RMA-normalize your data (using "affyrma" in Matlab)?

Regards,
Guido  

From: jerrych...@gmail.com [jerrych...@gmail.com]
Sent: Saturday, November 02, 2013 12:29 AM
To: aroma-affymetrix@googlegroups.com
Cc: jerrych...@gmail.com; Hooiveld, Guido
Subject: Re: [aroma.affymetrix] CDF file for Human Gene 1.1 st array

Hi Philip,
Thank you for your reply.  I am using MATLAB to analyze the gene expression 
data generated by "Affymetrix Human Gene 1.1-ST Array".  When I ran this 
function “affygcrma”, I got following error:

Warning: The ChipType (HuGene-1_1-st-v1) of CEL file
ASFREYT_HuGene1.1ST_C04_2.CEL does not match the ChipType
(HuGene-1_1-st-v1_ascii) of library file HuGene-1_1-st-v1_ascii.CDF.
> In celintensityread at 255
  In affygcrma at 140

Thanks,
Jerry

On Friday, November 1, 2013 3:20:09 PM UTC-7, philipg wrote:
Hi Jerry,

I read your message regarding the binary CDF that you downloaded from 
NuGO_R.html (I am responsible for these packages and I am the maintainer of 
NuGO_R.html). Unfortunately, you are not explaining what exactly the problems 
are that you encounter? Can you please explain to me what you are trying to do 
and in what kind of problems you run? I'll try to give you a hand then.

Regards,

Philip de Groot
Wageningen University


2013/11/1 
Hello,

To analyze Human Gene 1.1 st array, I used these CDF files, which are: 
HuGene-1_1-st-v1_ascii.CDF (from affymetrix) and (ii) 
HuGene-1_1-st-v1,byTranscript-fsetid,pd.hugene.1.1.st.v1.cdf (from 
http://nmg-r.bioinformatics.nl/NuGO_R.html).  Unfortunately, I am getting 
errors that stop me to move forward in my work.  Please let me know if there is 
another website to download this CDF file.
Thanks,
Jerry

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RE: [aroma.affymetrix] Re: Gene 2.0 ST arrays

2013-02-20 Thread Hooiveld, Guido

Hi Neetu,
I don't fully understand. I just re-downloaded the file through the link I 
mentioned before, and obtained a ZIP of 532MB. This ZIP contains 24 HuGene 2.0 
CEL files. Moreover, 24 HuGene 2.1 CEL files are included as well.
Indeed, I also concluded that yet no ST2.0 arrays are available through GEO. 
You have to realize that these 2.0 arrays are only on the market for less than 
a year or so, and it takes some time for labs to start using these chips, let 
alone to publish data that was generated. And it is only at that moment that 
submitting data to GEO or ArrayExpress is required.

Regards,
Guido

From: aroma-affymetrix@googlegroups.com 
[mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Neetu Tandon
Sent: Wednesday, February 20, 2013 11:37
To: aroma-affymetrix@googlegroups.com
Subject: Re: [aroma.affymetrix] Re: Gene 2.0 ST arrays

Thanks Guido. but the site says ' Sample data is no longer provided in 
individual files or in .CAB file format, and is thus not compatible with 
Microarray Suite (MAS) or with versions of GCOS that do not have DTT version 
1.1 or higher installed.

I will have to install many things to check if it is working properly. I would 
prefer if i get a dataset listed in GEO or ArrayExpress for testing my analysis 
method.
Is it possible that none of the publicly available datasets use this platform?

Thanks and Regards,
Neetu
On Wed, Feb 20, 2013 at 2:29 PM, Hooiveld, Guido 
mailto:guido.hooiv...@wur.nl>> wrote:
Hi,
You can obtain a set of sample HuGene 2.0 arrays directly from Affymetrix:
http://www.affymetrix.com/support/downloads/demo_data/human2_0.zip

Regards,
Guido

From: 
aroma-affymetrix@googlegroups.com<mailto:aroma-affymetrix@googlegroups.com> 
[mailto:aroma-affymetrix@googlegroups.com<mailto:aroma-affymetrix@googlegroups.com>]
 On Behalf Of Neetu Tandon
Sent: Wednesday, February 20, 2013 09:06
To: aroma-affymetrix@googlegroups.com<mailto:aroma-affymetrix@googlegroups.com>
Subject: [aroma.affymetrix] Re: Gene 2.0 ST arrays

Hello all,
It may be a little out of the current thread discussion, but i want to test a 
dataset which uses HuGene-1_0-st and HuGene-2_0-st arrays for my analysis tool 
in geneXplain platform.
I am getting lot of datasets using HuGene-1_0-st in GEO but not HuGene-2_0-st.
Can anyone help me with this. How should i get  publicly available dataset 
using this platform.
Is it also denoted by some other name.
Any pointers in this regard is really appreciated.

Thanks and Regards,
Neetu

On Thursday, 6 December 2012 19:24:58 UTC+5:30, Maria Traka wrote:
Hi guys,
probably you've already given the answer somewhere but can i use 
aroma.affymetrix to analyse Affymetrix 2.0 ST arrays (human and mouse)? 
Presumably the same way as 1.0 arrays?

Thanks in advance,
Maria
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traceback(), and 3) to post a complete code example.


You received this message because you are subscribed to the Google Groups 
"aroma.affymetr

RE: [aroma.affymetrix] Re: Gene 2.0 ST arrays

2013-02-20 Thread Hooiveld, Guido

Hi,
You can obtain a set of sample HuGene 2.0 arrays directly from Affymetrix:
http://www.affymetrix.com/support/downloads/demo_data/human2_0.zip

Regards,
Guido

From: aroma-affymetrix@googlegroups.com 
[mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Neetu Tandon
Sent: Wednesday, February 20, 2013 09:06
To: aroma-affymetrix@googlegroups.com
Subject: [aroma.affymetrix] Re: Gene 2.0 ST arrays

Hello all,
It may be a little out of the current thread discussion, but i want to test a 
dataset which uses HuGene-1_0-st and HuGene-2_0-st arrays for my analysis tool 
in geneXplain platform.
I am getting lot of datasets using HuGene-1_0-st in GEO but not HuGene-2_0-st.
Can anyone help me with this. How should i get  publicly available dataset 
using this platform.
Is it also denoted by some other name.
Any pointers in this regard is really appreciated.

Thanks and Regards,
Neetu

On Thursday, 6 December 2012 19:24:58 UTC+5:30, Maria Traka wrote:
Hi guys,
probably you've already given the answer somewhere but can i use 
aroma.affymetrix to analyse Affymetrix 2.0 ST arrays (human and mouse)? 
Presumably the same way as 1.0 arrays?

Thanks in advance,
Maria
--
--
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version of the package, 2) to report the output of sessionInfo() and 
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[aroma.affymetrix] binary CDF files on-line

2013-01-22 Thread Hooiveld, Guido

Hi all,
This is to inform you that (finally) we have put on-line the binary CDFs for 18 
arrays. Please find them on our server (Table 4):
http://nmg-r.bioinformatics.nl/NuGO_R.html

CDFs are available for these arrays:
AraGene-1_0-st
AraGene-1_1-st
HuGene-1_0-st-v1
HuGene-1_1-st-v1
HuGene-2_0-st
HuGene-2_1-st
MoGene-1_0-st-v1
MoGene-1_1-st-v1
MoGene-2_0-st
MoGene-2_1-st
PorGene-1_0-st
PorGene-1_1-st
RaGene-1_0-st-v1
RaGene-1_1-st-v1
RaGene-2_0-st
RaGene-2_1-st
ZebGene-1_0-st
ZebGene-1_1-st

>From the readme.txt:
- This binary CDF has been created from a platform design info (PdInfo) package 
available in R version 2.15.2/ Bioconductor version 2.11 using functions 
available the library aroma.affymetrix v2.8.0.
- 'Probesets' are based on transcript clusters (meta-probeset) as defined by 
Affymetrix in the MPS (meta probeset) file, as is also reflected in the 
filename.
- A transcript cluster is a group of one or more probes covering a region of 
the genome reflecting all the exonic transcription evidence known for the 
region and corresponding to a known or putative gene. The underlying exonic 
evidence can come from transcripts of well-annotated genes or predicted genes. 
A given transcript cluster may have a variety of assigned RNAs, classified 
according to the NetAffx transcript classification system.
- Please note that these are unofficial CDFs (i.e. CDF files not supported or 
endorsed by Affymetrix), so you agree to use them at your own risk! However, 
whenever possible*, binary CDFs have been confirmed to be working with 
aroma.affymetrix.
- In principle the binary CDFs could also be used with stand-alone applications 
such as dChip. Unfortunately, at the moment of writing, dChip is not able to 
load these files. The author of dChip has been informed about this, but 
currently no fix is available.
- Please post on the aroma.affymetrix mailing list if you have problems using 
these files. [http://www.aroma-project.org/]
- Files have been created in January 2013.

* In case of available CEL files.

Hope these are uselful! :)

Regards,
Guido


-
Guido Hooiveld, PhD
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
Wageningen University
Biotechnion, Bomenweg 2
NL-6703 HD Wageningen
the Netherlands
tel: (+)31 317 485788
fax: (+)31 317 483342
email:  guido.hooiv...@wur.nl
internet:   http://nutrigene.4t.com
http://scholar.google.com/citations?user=qFHaMnoJ
http://www.researcherid.com/rid/F-4912-2010

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RE: [aroma.affymetrix] Affymetrix Gene 2.0 ST-array cdf files for Human, Mouse and rat.

2013-01-17 Thread Hooiveld, Guido

Hi,
The binary CDFs are not uploaded yet**. I'll do so tomorrow (Friday). On our 
server indeed only CDF environments for use in R are currently available.
Guido

**Reason for the delay: I have indeed confirmed that the binary CDFs work as 
expected with aroma.affymetrix. Since these binary CDFs could (in principle) 
also be used with 'stand-alone' applications such as dChip, I checked whether 
dChip likes these files as well. Unfortunately, this seems not to be the case 
(yet?). I have contacted the dChip developer to ask what could be the cause of 
this, and whether this could be fixed, but this hasn't resulted yet in a fix. 
Hence, I put on hold the release of these files until someone really needed 
these (hoping that in the meantime the dChip issue could be addressed).

From: aroma-affymetrix@googlegroups.com 
[mailto:aroma-affymetrix@googlegroups.com] On Behalf Of rangerq
Sent: Thursday, January 17, 2013 20:44
To: aroma-affymetrix@googlegroups.com
Subject: [aroma.affymetrix] Affymetrix Gene 2.0 ST-array cdf files for Human, 
Mouse and rat.

Hello,

Do anyone have the cdf files for Affymetrix Human, mouse or rat Gene 2.0 
ST-arrays? Could you share them?

I tried to use the one that Guido mentioned at http://nmg-r.bioinformatics.nl/ 
but it is not a file that can be directly read by Aroma.affymetrix package.

It is a R package that I can load it in R but do not know how to use it within 
Aroma.affymetirx.

Thanks,
Qihao QI
EMMES Crop.
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[aroma.affymetrix] Error in if (hasTimestamp) { : argument is of length zero

2012-12-10 Thread Hooiveld, Guido

Hi Henrik,

I am testing the binary CDF files I created for various Gene ST arrays (re: 
discussion last Friday), but I run into problems.
An error is occurring when reading the cell files. According to the change log 
this error has been reported before and should have been fixed by you (in 
version: 2.1.9 [2011-08-31]), so I don't know why this is happening. Could you 
please have a look?

This error occurs when trying to load mouse Gene ST v1.1 arrays; both in-house 
generated files as well as the ones downloaded from Affymetrix 
(http://www.affymetrix.com/support/downloads/demo_data/gene_1_1_st_ap_tissue_sample_data.zip).
 Idem for Affy-provided sample Gene ST v2.1 arrays.
Remarkably, loading Gene ST v1.0 arrays goes fine... (I haven't tested any 
other array types yet).

See below for code & output (first STv1.0 (=working); followed by STv1.1 
(=failing)).

Regards,
Guido

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



# Gene ST v1.0 arrays (working)
> chipType <- "MoGene-1_0-st-v1"
>
> cdf <- AffymetrixCdfFile$byChipType(chipType)
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/MoGene-1_0-st-v1
Filename: MoGene-1_0-st-v1.cdf
File size: 16.69 MB (17500618 bytes)
Chip type: MoGene-1_0-st-v1
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 1050x1050
Number of cells: 1102500
Number of units: 28857
Cells per unit: 38.21
Number of QC units: 0
> cs <- AffymetrixCelSet$byName("guido", cdf=cdf);
> cs
AffymetrixCelSet:
Name: guido
Tags:
Path: rawData/guido/MoGene-1_0-st-v1
Platform: Affymetrix
Chip type: MoGene-1_0-st-v1
Number of arrays: 5
Names: A176_01_MCOLON_CD0_P1, A176_02_MCOLON_CD2_P2, A176_03_MCOLON_CD4_P3, 
A176_04_MCOLON_CD7_P4, A176_05_MCOLON_CD14_P5 [5]
Time period: 2010-01-29 11:45:08 -- 2010-01-29 12:20:51
Total file size: 52.79MB
RAM: 0.01MB
>

# Check CEL HEADER (using library AffxParser)
> files <- list.files(pattern="[.](c|C)(e|E)(l|L)$")
>   if (length(files) > 0) {
+ header <- readCelHeader(files[1])
+ print(header)
+ rm(header)
+   }
$filename
[1] "./A176_01_MCOLON_CD0_P1.CEL"

$version
[1] 4

$cols
[1] 1050

$rows
[1] 1050

$total
[1] 1102500

$algorithm
[1] "Percentile"

$parameters
[1] 
"Percentile:75;CellMargin:4;OutlierHigh:1.500;OutlierLow:1.004;AlgVersion:6.0;FixedCellSize:TRUE;FullFeatureWidth:7;FullFeatureHeight:7;IgnoreOutliersInShiftRows:FALSE;FeatureExtraction:TRUE;PoolWidthExtenstion:1;PoolHeightExtension:1;UseSubgrids:TRUE;RandomizePixels:FALSE;ErrorBasis:StdvMean;StdMult:1.00;NumDATSubgrids:36"

$chiptype
[1] "MoGene-1_0-st-v1"

$header
[1] 
"Cols=1050\nRows=1050\nTotalX=1050\nTotalY=1050\nOffsetX=0\nOffsetY=0\nGridCornerUL=360
 273\nGridCornerUR=7866 311\nGridCornerLR=7821 7775\nGridCornerLL=315 
7737\nAxis-invertX=0\nAxisInvertY=0\nswapXY=0\nDatHeader=[1..20525]  
A176_01_mColon_cd0_p1:CLS=8341 RWS=8341 XIN=0  YIN=0  VE=302.0 01/29/10 
11:45:08 50209050  M10   \024  \024 MoGene-1_0-st-v1.1sq \024  \024  \024  \024 
 \024 570 \024 25434.212891 \024 3.50 \024 0.7000 \024 
3\nAlgorithm=Percentile\nAlgorithmParameters=Percentile:75;CellMargin:4;OutlierHigh:1.500;OutlierLow:1.004;AlgVersion:6.0;FixedCellSize:TRUE;FullFeatureWidth:7;FullFeatureHeight:7;IgnoreOutliersInShiftRows:FALSE;FeatureExtraction:TRUE;PoolWidthExtenstion:1;PoolHeightExtension:1;UseSubgrids:TRUE;RandomizePixels:FALSE;ErrorBasis:StdvMean;StdMult:1.00;NumDATSubgrids:36\n"

$datheader
[1] "[1..20525]  A176_01_mColon_cd0_p1:CLS=8341 RWS=8341 XIN=0  YIN=0  VE=30
2.0 01/29/10 11:45:08 50209050  M10   \024  \024 MoGene-1_0-st-v1.1sq \024  
\024  \024  \024  \024 570 \024 25434.212891 \024 3.50 \024 0.7000 \024 3"

$librarypackage
[1] ""

$cellmargin
[1] 4

$noutliers
[1] 12644

$nmasked
[1] 0

>

#Gene ST V1.1 arrays (fails)
> chipType <- "MoGene-1_1-st-v1"
>
> cdf <- AffymetrixCdfFile$byChipType(chipType)
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/MoGene-1_1-st-v1
Filename: MoGene-1_1-st-v1.cdf
File size: 16.69 MB (17500604 bytes)
Chip type: MoGene-1_1-st-v1
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 1190x990
Number of cells: 1178100
Number of units: 28857
Cells per unit: 40.83
Number of QC units: 0
> cs <- AffymetrixCelSet$byName("guido", cdf=cdf)
> cs
Error in if (hasTimestamp) { : argument is of length zero
>

# Check CEL HEADER
> files <- list.files(pattern="[.](c|C)(e|E)(l|L)$")
>   if (length(files) > 0) {
+ header <- readCelHeader(files[1])
+ print(header)
+ rm(header)
+   }
$filename
[1] "./G065_A05_02_TW188_344.CEL"

$version
[1] 1

$cols
[1] 990

$rows
[1] 1190

$total
[1] 1178100

$algorithm
[1] "HT Image Calibration Cell Generation"

$parameters
[1] 
"NumPixelsToUse:4;ImageCalibration:TRUE;FeatureExtraction:FALSE;IgnoreShiftRowOutliers:FALSE;FixedCellSize:TRUE;UseSubgrids:FALSE;RandomizePixels:FALSE;ErrorBasis:StdvMean;PercentileSpread:15.00;StdMult:1.00;ExtendPoolWidth:2;ExtendPoolHeight:2;OutlierLow:1.004000;OutlierHigh:1.50;OutlierRatioLowPercentile:55;OutlierRatioHighPercentile:75;Cell

RE: [aroma.affymetrix] Gene 2.0 ST arrays

2012-12-07 Thread Hooiveld, Guido

Hi,
Sorry for the indistinctness. You are correct; these are indeed R-packages (CDF 
environments), thus not *files*. However, it won't be much effort to also make 
them available as files. I/we will have a look at it the next couple of days. 
We will also check the links/info and update them when needed.
Guido 

-Original Message-
From: aroma-affymetrix@googlegroups.com 
[mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Henrik Bengtsson
Sent: Friday, December 07, 2012 17:51
To: aroma-affymetrix@googlegroups.com
Subject: Re: [aroma.affymetrix] Gene 2.0 ST arrays

Hi.

On Fri, Dec 7, 2012 at 5:21 AM, Hooiveld, Guido  wrote:
> Hi,
> To follow up on Henrik's suggestion: we recently have made 
> Bioconductor-compatible ('unofficial') CDFs for the STv2.0/2.1 arrays as 
> well, essentially using the PD.Info packages. Please find them here:
> http://nmg-r.bioinformatics.nl/

This great.  To clarify, are you creating/releasing CDF *files*, or only the 
various flavors of R packages containing that information?
I see that you are referring to 'PdInfo2Cdf.R'(*) on the site, which indicates 
CDF files, but I cannot find such.  (*) BTW, that script has now been replaced 
by http://aroma-project.org/howtos/createCdfFromBioconductorPlatformDesignInfo

Thanks,

Henrik

> HTH,
> Guido
>
> -Original Message-
> From: aroma-affymetrix@googlegroups.com 
> [mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Henrik 
> Bengtsson
> Sent: Thursday, December 06, 2012 21:45
> To: aroma-affymetrix@googlegroups.com
> Subject: Re: [aroma.affymetrix] Gene 2.0 ST arrays
>
> On Thu, Dec 6, 2012 at 5:54 AM, Maria Traka  wrote:
>> Hi guys,
>> probably you've already given the answer somewhere but can i use 
>> aroma.affymetrix to analyse Affymetrix 2.0 ST arrays (human and mouse)?
>> Presumably the same way as 1.0 arrays?
>
> I'm not working with those myself, and I don't know the exact design details 
> on those chips, but, yes, most likely the same way as the previous ST arrays.
>
> What is not available out of the box is a CDF file for these 2.0 ST 
> arrays (i.e. HuGene-2_0-st-v1 and ).  Unless you find such CDFs from 
> the various groups providing custom CDFs, you need to create them 
> yourselves.  Here you've got a few options, but I would try with 
> what's explained in how-to page 'Create a CDF file from Bioconductor 
> Platform Design (PD) Info package', which you find via 
> http://aroma-project.org/howtos/
>
> /Henrik
>
>>
>> Thanks in advance,
>> Maria
>>
>> --
>> 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 
> "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.


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-- 
When r

RE: [aroma.affymetrix] Gene 2.0 ST arrays

2012-12-07 Thread Hooiveld, Guido

Hi,
To follow up on Henrik's suggestion: we recently have made 
Bioconductor-compatible ('unofficial') CDFs for the STv2.0/2.1 arrays as well, 
essentially using the PD.Info packages. Please find them here:
http://nmg-r.bioinformatics.nl/
HTH,
Guido

-Original Message-
From: aroma-affymetrix@googlegroups.com 
[mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Henrik Bengtsson
Sent: Thursday, December 06, 2012 21:45
To: aroma-affymetrix@googlegroups.com
Subject: Re: [aroma.affymetrix] Gene 2.0 ST arrays

On Thu, Dec 6, 2012 at 5:54 AM, Maria Traka  wrote:
> Hi guys,
> probably you've already given the answer somewhere but can i use 
> aroma.affymetrix to analyse Affymetrix 2.0 ST arrays (human and mouse)?
> Presumably the same way as 1.0 arrays?

I'm not working with those myself, and I don't know the exact design details on 
those chips, but, yes, most likely the same way as the previous ST arrays.

What is not available out of the box is a CDF file for these 2.0 ST arrays 
(i.e. HuGene-2_0-st-v1 and ).  Unless you find such CDFs from the various 
groups providing custom CDFs, you need to create them yourselves.  Here you've 
got a few options, but I would try with what's explained in how-to page 'Create 
a CDF file from Bioconductor Platform Design (PD) Info package', which you find 
via http://aroma-project.org/howtos/

/Henrik

>
> Thanks in advance,
> Maria
>
> --
> 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/

--
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RE: [aroma.affymetrix] aroma.affymetrix v2.1.0 released

2011-04-11 Thread Hooiveld, Guido

Hi Henrik,

Thanks for your continuous efforts on aroma.affymetrix!

With interest I have read the change-log, but do you mind spending a few words 
what exactly is meant with this argument, and why this is implemented?
o Added argument 'uniquePlm' to doRMA() and doGCRMA() for doing
  probe-level summarization on unique probe sets only.

I looked up the source code to see what exactly will happen when this argument 
is passed, but i wasn't able to fully understand it. I guess it is related to 
this thread at the BioC mailing list?
http://article.gmane.org/gmane.science.biology.informatics.conductor/33688
 
Thanks & regards,
Guido


- 
Guido Hooiveld, PhD 
Nutrition, Metabolism & Genomics Group 
Division of Human Nutrition 
Wageningen University 
Biotechnion, Bomenweg 2 
NL-6703 HD Wageningen 
the Netherlands 
tel: (+)31 317 485788 
fax: (+)31 317 483342 
email:  guido.hooiv...@wur.nl
internet:   http://nutrigene.4t.com 
http://www.researcherid.com/rid/F-4912-2010


-Original Message-
From: aroma-affymetrix@googlegroups.com 
[mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Henrik Bengtsson
Sent: Monday, April 11, 2011 21:39
To: aroma-affymetrix
Subject: [aroma.affymetrix] aroma.affymetrix v2.1.0 released

Hi,

aroma.affymetrix v2.1.0 and friends have been released.  Grab the new version 
by:

source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");



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version of the package, 2) to report the output of sessionInfo() and 
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RE: [aroma.affymetrix] Re: writeCdf.AffyGenePDInfo Error in order(u$atom): argument 1 is not a vector

2011-01-28 Thread Hooiveld, Guido

Hi,
In addition to Henrik's remarks, I also would like to comment:
- Entrez Gene-based remapped CDFs (the ones from MNBI) are normally used for 
the analyses fo expression arrays; the array type you would like to analyse is 
not such an array! That's the reason the coverage is so little!
- you have an error in this line of code:
t250knsp <- ReadAffy(cdfname="mapping250knsphsentrezgcdf")
should rather be:
t250knsp <- ReadAffy(cdfname="mapping250knsphsentrezg")
(thus NOT ending on 'cdf')
- Although this is the aroma.affymetrix, please allow me to say that the 
library 'oligo' available on BioC likely is able to do what you want. As Henrik 
said, 'oligo' used info directly derived from Affymetrix, and this is 
apparently what you want.

HTH,
Guido

 

 
Guido Hooiveld, PhD 
Nutrition, Metabolism & Genomics Group 
Division of Human Nutrition 
Wageningen University 
Biotechnion, Bomenweg 2 
NL-6703 HD Wageningen 
the Netherlands 
tel: (+)31 317 485788 
fax: (+)31 317 483342 
email:  guido.hooiv...@wur.nl
internet:   http://nutrigene.4t.com 
http://www.researcherid.com/rid/F-4912-2010



-Original Message-
From: aroma-affymetrix@googlegroups.com 
[mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Henrik Bengtsson
Sent: Friday, January 28, 2011 21:08
To: aroma-affymetrix
Subject: Re: [aroma.affymetrix] Re: writeCdf.AffyGenePDInfo Error in 
order(u$atom): argument 1 is not a vector

Hi,

ok, so I didn't understand you didn't want to use the aroma framework for your 
analysis.  Now I understand that you are only trying to create a CDF *file* 
from a PDInfo package, and continue elsewhere.

However, I still don't follow.  From which PDInfo package do you want to create 
a CDF file?  The default one (pd.mapping250k.nsp) provided by Bioconductor as 
your initial post used, or another one?  To the best of my knowledge, the 
'pd.mapping250k.nsp' was created from the original Affymetrix CDF among other 
files, that is, at
writeCdf(pd.mapping250k.nsp) would generate a CDF file identical to the 
original Affymetrix CDF.

You can look into the code of writeCdf(), read about the Affymetrix CDF file 
format (cf. affxparser package), and probably also the Bioconductor PDInfo code 
to see what is causing the problem.  However, I believe you're better of asking 
for help on the Bioconductor community, because what you are trying to solve 
does not seem to be aroma related.

Cheers,

/Henrik

PS. BTW, It should be writeCdf(pd.mapping250k.nsp) not 
writeCdf.AffyGenePDInfo(pd.mapping250k.nsp).  That's how method dispatching 
works under the S3 class model in R.


On Fri, Jan 28, 2011 at 11:50 AM, Sake van Pelt  
wrote:
> Thanks for the quick response!
>
> The reason behind this problem came from a project I am working on. I 
> want to analyze Affymetrix 250k_nsp data in R, but there is no 
> suitable annotation cdf package available. On this moment I am using 
> an alternative cdf package from the brainarray website (http:// 
> brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/13.0.0/
> entrezg.asp) annotated with the entrezg database. This package 
> however, has only 0.8% (2803) of the originally amount of over 3.2 
> million probes, so a lot of valuable data is lost that way. I will 
> show some of my code here:
>
>>library(affy)
>>library(limma)
>>library(mapping250knsphsentrezgcdf)
>>library(mapping250knsphsentrezg.db)
>>library(mapping250knsphsentrezgprobe)
>
>>setwd("/data/home/pavandervelden/Minor/Tumor")
>>t250knsp <- ReadAffy(cdfname="mapping250knsphsentrezgcdf")
>
> With 'ReadAffy' it is not possible to use a cdf file that is not 
> installed as a package, only cdf environments are allowed. There comes 
> the reason why I cannot use the cdf files provided by Affymetrix, when 
> I want to make a cdf environment with those cdf files I keep on 
> getting messages that it is not a real cdf file (CustomCDF package 
> from brainarray), or that it cannot be read the right way. Usage of 
> the 'pd.mapping250k.nsp' package is also not an option in this method.
> Shortly said: I want to build an full annotation package set (cdf 
> package, probe package and .db package) with the original, untouched 
> data from Affymetrix and I hoped to create a cdf file that would be 
> accepted by the functions that were able to create a cdf environment 
> in R. Maybe that is possible wit the aroma package, but I did not find 
> out a way how. I think it is because it isn't a expression array, but 
> I hope i am wrong and that it IS possible.
>
> I hope you can help me!
>
> Kind regards,
> Sake van Pelt
>
>
>
> On 28 jan, 19:34, Henrik Bengtsson  project.org> wrote:
>> Hi,
>>
>> before anything else, what are the problems you're experiencing with 
>> the official Affymetrix CDF file:
>>
>> > I know I can download a cdf file from the Affymetrix website, but 
>> > that file doesn't work for me..
>>
>> That CDF has been used for many year and yet I haven't heard anyone 
>> e

[aroma.affymetrix] bug in function pdInfo2Cdf

2010-12-03 Thread Hooiveld, Guido

Dear Henrik,

I would like to report a problem with the function pdInfo2Cdf.R
I know this function is not part of the core functionality of aroma.affymetrix, 
but i thought it still would be good to inform you about the error i found.
Meanwhile I found out it is caused by line 71:
the argument 'pdName' should actually be 'pdpkg' in
line 71 - filename <- sprintf("%s.cdf", pdName);

If I apply the above-mentioned modification, source the modified function 
'pdInfo2Cdf_MOD.R, and then run the function everything goes fine (see below).

For your convenience I have uploaded a CEL file required to execute the 
function (for testing purposes):
https://sendit.wur.nl/Download.aspx?id=e0c9eea2-5f72-454c-873d-f1a215f57d1c
Note: link is alive for 5 days, and/or allows max 20 downloads.

Regards,
Guido


> library(aroma.affymetrix)
<>
> pdInfo2Cdf("pd.mogene.1.1.st.v1", "MouseBrain_1.CEL");
<>
PdInfo2Cdf()...
Error in sprintf("%s.cdf", pdName) : object 'pdName' not found
In addition: Warning message:
In fcn(...) : Packages reordered in search path: package:oligo

> source("pdInfo2Cdf_MOD.R")
> pdInfo2Cdf("pd.mogene.1.1.st.v1", "MouseBrain_1.CEL");
PdInfo2Cdf()...
Loading required package: pd.mogene.1.1.st.v1
 Reading auxillary CEL file...
Platform design info loaded.
Reading in : MouseBrain_1.CEL
 Reading auxillary CEL file...done
 Querying Platform Design database...
 Querying Platform Design database...done
 Creating list from query table...
 Creating list from query table...done
 Creating CDF list structure...
  Creating CDF list for 241576 units
 Creating CDF list structure...done
 Writing CDF file...
Writing CDF file...
  Pathname: pd.mogene.1.1.st.v1.cdf
  Writes CDF header and unit names...
  Writes CDF header and unit names...done
  Writes QC units...
  Writes QC units...done
  Writes 241576 units...
  Writes 241576 units...done
Writing CDF file...done
 Writing CDF file...done
PdInfo2Cdf()...done
>
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C  LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] pdInfoBuilder_1.14.1   oligoClasses_1.12.1RSQLite_0.9-4
 [4] DBI_0.2-5  Biobase_2.10.0 aroma.affymetrix_1.8.0
 [7] aroma.apd_0.1.7affxparser_1.22.0  R.huge_0.2.0
[10] aroma.core_1.8.0   aroma.light_1.18.2 matrixStats_0.2.2
[13] R.rsp_0.4.0R.cache_0.3.0  R.filesets_0.9.1
[16] digest_0.4.2   R.utils_1.5.8  R.oo_1.7.4
[19] oligo_1.14.0   R.methodsS3_1.2.1

loaded via a namespace (and not attached):
[1] affyio_1.19.2 Biostrings_2.18.0 IRanges_1.8.3
[4] preprocessCore_1.12.0 splines_2.12.0

Guido Hooiveld, PhD
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
Wageningen University
Biotechnion, Bomenweg 2
NL-6703 HD Wageningen
the Netherlands
tel: (+)31 317 485788
fax: (+)31 317 483342
internet:   http://nutrigene.4t.com
email:  guido.hooiv...@wur.nl

-- 
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: PdInfo2Cdf function

2010-04-23 Thread Hooiveld, Guido

Sorry to bother you again, but oops, I made a mistake copy/pasting the code of 
the modified function...
(query command to be specific).

This is correct:

PdInfo2Cdf <- function( pdpkg, celfile, verbose=TRUE, overwrite=FALSE ) {

   This script has been written to generate a .cdf-file from an "pd." 
package,
   such as those build with pdInfoBuilder.
   The original was written by Samuel Wuest, modified by Mark Robinson
   (around 12 Jan 2009) to be generic

  require("affxparser") || stop("Package not loaded: affxparser");
  require("pdInfoBuilder") || stop("Package not loaded: pdInfoBuilder");

  do.call("library",args=list(package=pdpkg))

  pmFeature2List <- function(u) {
nr <- nrow(u)
o <- order(u$atom)
v <- 0:(nr-1)
#id <- u$fsetid[1]
id <- u$meta_fsetid[1]
g <- list(list(x=u$x[o], y=u$y[o], pbase=rep("T",nr),tbase=rep("A",nr),
  
atom=v,indexpos=v,groupdirection="sense",natoms=nr,ncellsperatom=1))
names(g) <- id

list(unittype=1,unitdirection=1,groups=g,natoms=nr,ncells=nr,ncellsperatom=1,unitnumber=id)
  }

  if(verbose)
cat("Reading CEL file.\n")
  cel <- read.celfiles(filenames=celfile,pkgname=pdpkg)
  pd <-getPlatformDesign(cel)
  if(verbose)
cat("Querying Platform Design database.\n")
  #ff <- dbGetQuery(db(pd), "select * from pmfeature") # gives probesets/exons
  ff <- dbGetQuery(db(pd), "SELECT fid, meta_fsetid, atom, x, y FROM pmfeature 
INNER JOIN core_mps USING(fsetid)") #gives meta-probesets/transcripts


  celHead <- readCelHeader(celfile)
  nrows <- celHead$rows
  ncols <- celHead$rows


  # three 3 lines speed up the splitting ...
  if(verbose)
cat("Creating list from query table.\n")
  #ffs <- split(ff, substr(ff$fsetid,1,4))
  ffs <- split(ff, substr(ff$meta_fsetid,1,4))
  #ffs <- unlist( lapply(ffs, FUN=function(u) split(u,u$fsetid)), 
recursive=FALSE)
  ffs <- unlist( lapply(ffs, FUN=function(u) split(u,u$meta_fsetid)), 
recursive=FALSE)
  names(ffs) <- substr(names(ffs), 6,nchar(names(ffs)))

  nunits <- length(ffs)

  pdName <- gsub("\\.","",pdpkg)

  ## creating the cdf-header;
  newCdfHeader <- list(ncols=ncols, nrows=nrows, nunits=nunits, nqcunits=0, 
refseq="",
   chiptype=pdName, filename=paste(pdName,"cdf",sep="."), 
rows=nrows,
   cols=ncols, probesets= nunits, qcprobesets= 0, 
reference="")

  ### make the input-list for the writeCdf-function
  if(verbose)
cat(paste("Creating CDF list for", nunits, "units.\n"))
  newCdfList <- lapply(ffs, pmFeature2List)

  ### writing the cdf-file (binary-file)
  writeCdf(newCdfHeader$filename, cdfheader= newCdfHeader, cdf=newCdfList, 
cdfqc=NULL, verbose=verbose, overwrite=overwrite)

}







> -Original Message-
> From: aroma-affymetrix@googlegroups.com
> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of
> Hooiveld, Guido
> Sent: 23 April 2010 22:48
> To: 'aroma-affymetrix@googlegroups.com'; 'Mark Robinson'
> Subject: [aroma.affymetrix] RE: PdInfo2Cdf function
>
> Hello Mark and list,
> We have finally gotten things to work and I am replying to
> this email for archive purposes in case someone else is interested.
>
> Wrapping up:
> For obvious reasons (better support for arrays that do have a
> corresponding CDF file, both in BioC as well as other
> softwares) the challenge was how to create a (binary) CDF
> file for the Affymetrix Human/Mouse/Rat Gene ST arrays,
> either v1.0 (cardridge array) or v1.1 (GeneTitan arrays),
> that used the transcript-clusters (aka meta-probesets) as
> unit (instead of exons (aka probesets)).
> http://www.affymetrix.com/support/help/exon_glossary/index.affx
> To illustrate this, according to Affy's annotation r4 the
> mouse Gene ST array v1.0
> [http://www.affymetrix.com/estore/browse/products.jsp?productI
> d=131476&categoryId=35765] contains 899,635 probes that form
> 241,576 probesets (exons) that detect 35,556 meta-probesets
> (transcript clusters).
>
> The function PdInfo2Cdf.R Mark kindly made availabe through
> aroma.affymetrix webpage is able to make such CDF file taking
> the platform design files used by the BioC package 'oligo'
> (and a CEL file) as input, however, only at the level of
> probesets (exons). The challenge was to modify the function
> such way that a CDF could be created that was based on the
> 35,556 metaprobesets.
>
> As was indicated by Mark, the key to this was to query the
> database (e.g. pd.mogene.1.1.st.v1) slightly different.
> In the PdInfo2CDF.R function the line:
> ff <- dbGetQuery(d

[aroma.affymetrix] RE: PdInfo2Cdf function

2010-04-23 Thread Hooiveld, Guido

tr(names(ffs), 6,nchar(names(ffs)))

  nunits <- length(ffs)

   pdName <- gsub("\\.","",pdpkg)

  ## creating the cdf-header;
  newCdfHeader <- list(ncols=ncols, nrows=nrows, nunits=nunits, nqcunits=0, 
refseq="",
   chiptype=pdName, filename=paste(pdName,"cdf",sep="."), 
rows=nrows,
   cols=ncols, probesets= nunits, qcprobesets= 0, 
reference="")

  ### make the input-list for the writeCdf-function
  if(verbose)
cat(paste("Creating CDF list for", nunits, "units.\n"))
  newCdfList <- lapply(ffs, pmFeature2List)

  ### writing the cdf-file (binary-file)
  writeCdf(newCdfHeader$filename, cdfheader= newCdfHeader, cdf=newCdfList, 
cdfqc=NULL, verbose=verbose, overwrite=overwrite)

}







> source("PdInfo2Cdf_modified.R")
> PdInfo2Cdf("pd.mogene.1.1.st.v1", "G002_C05_9_FENOFIBRATE.CEL", 
> overwrite=TRUE);
Loading required package: pdInfoBuilder
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: RSQLite
Loading required package: DBI
Loading required package: oligo
Loading required package: oligoClasses

Welcome to oligoClasses version 1.10.0

Large dataset support for 'oligo/crlmm': Disabled
 - Load 'ff'

Parallel computing support for 'oligo/crlmm': Disabled
 - Load 'ff'
 - Load 'snow'
 - Use options(cluster=makeCluster(...))


Welcome to oligo version 1.12.0

Reading CEL file.
Platform design info loaded.
Reading in : G002_C05_9_FENOFIBRATE.CEL
Querying Platform Design database.
Creating list from query table.
Creating CDF list for 35556 units.
Writing CDF file...
  Pathname: pdmogene11stv1.cdf
  Writes CDF header and unit names...
  Writes CDF header and unit names...done
  Writes QC units...
  Writes QC units...done
  Writes 35556 units...
  Writes 35556 units...done
Writing CDF file...done
>
>
> sessionInfo()
R version 2.11.0 RC (2010-04-18 r51771)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C  LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] pd.mogene.1.1.st.v1_3.0.1 pdInfoBuilder_1.12.0
[3] oligo_1.12.0  oligoClasses_1.10.0
[5] RSQLite_0.8-4 DBI_0.2-5
[7] Biobase_2.7.6 affxparser_1.19.6

loaded via a namespace (and not attached):
[1] affyio_1.15.2Biostrings_2.15.27   IRanges_1.5.79
[4] preprocessCore_1.9.0 splines_2.11.0   tools_2.11.0
>



> -Original Message-
> From: aroma-affymetrix@googlegroups.com
> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of
> Hooiveld, Guido
> Sent: 21 April 2010 21:08
> To: 'Mark Robinson'
> Cc: 'aroma-affymetrix@googlegroups.com'
> Subject: [aroma.affymetrix] RE: PdInfo2Cdf function
>
> Hi Mark (and others on the list),
>
> Thanks for your reply. A collegue and I worked on this and we
> believe we are *almost* there; unfortunately creating a CDF
> environment from the the resulting binary CDF fails...
> Hopefully you could give us an hint to really complete the
> exercise. :)
>
> Indeed, generating the pd.**.1.1.st.v1 packages goes fine
> (and are meanwhile also availabe on BioC development).
> We checked the source code from the oligo library and found
> the lines that are used to query the pd-RSQL database to
> retrieve the meta-probeset definitions.
>
> From the source of Dr Carvalho's package Oligo,
> 'utils-general.R', section "## Selectors for probes - useful
> for exon/gene arrays"
> Function describing our need: 'getFidMetaProbesetCore'.
> Copy/paste:
> getFidMetaProbesetCore <- function(object){
>   conn <- db(object)
>   sql <- "SELECT fid, meta_fsetid as fsetid FROM pmfeature
> INNER JOIN core_mps USING(fsetid)"
>   featureInfo <-

[aroma.affymetrix] RE: PdInfo2Cdf function

2010-04-21 Thread Hooiveld, Guido

o <- order(u[,1])
v <- 0:(nr-1)
id <- u$fsetid[1]
g <- list(list(x=u$x[o], y=u$y[o], pbase=rep("T",nr),tbase=rep("A",nr),
  
atom=v,indexpos=v,groupdirection="sense",natoms=nr,ncellsperatom=1))
names(g) <- id

list(unittype=1,unitdirection=1,groups=g,natoms=nr,ncells=nr,ncellsperatom=1,unitnumber=id)
  }

  if(verbose)
cat("Reading CEL file.\n")
  cel <- read.celfiles(filenames=celfile,pkgname=pdpkg)
  pd <-getPlatformDesign(cel)
  if(verbose)
cat("Querying Platform Design database.\n")

## below replaced original query of probesest by query of meta-probesets
# original: ff <- dbGetQuery(db(pd), "select * from pmfeature")
# Below from oligo package, utils-general; function "getFidMetaProbesetCore"
object <- pd
conn <- db(object)
  sql <- "SELECT fid, meta_fsetid as fsetid FROM pmfeature INNER JOIN core_mps 
USING(fsetid)"
  featureInfo <- dbGetQuery(conn, sql)
  featureInfo <- featureInfo[order(featureInfo[["fsetid"]]),]
  rownames(featureInfo) <- NULL
  #return(featureInfo)

ff <- featureInfo
## END MODIFICATION
  

  celHead <- readCelHeader(celfile)
  nrows <- celHead$rows
  ncols <- celHead$rows


  # three 3 lines speed up the splitting ...
  if(verbose)
cat("Creating list from query table.\n")
  ffs <- split(ff, ff$fsetid)
  #ffs <- split(ff, substr(ff$fsetid,1,4))  ##<<-- replaced this line with 
line above since 
##we otherwise 
only ended up with around 290 

##meta-probesets. Unfortunately, our approach 
##now takes 
quite some some time...
  #ffs <- unlist( lapply(ffs, FUN=function(u) split(u,u$fsetid)), 
recursive=FALSE)
  #names(ffs) <- substr(names(ffs), 6,nchar(names(ffs)))

  nunits <- length(ffs)

#  pdName <- gsub("\\.","",pdpkg)
   pdName <- "hugene10stv1" #for now just worked with the human Gene ST v1.0 
array, since there  
#is an unoffical CDF available (= 
'positive' control)

  ## creating the cdf-header;
  newCdfHeader <- list(ncols=ncols, nrows=nrows, nunits=nunits, nqcunits=0, 
refseq="", 
   chiptype=pdName, filename=paste(pdName,"cdf",sep="."), 
rows=nrows, 
   cols=ncols, probesets= nunits, qcprobesets= 0, 
reference="")

  ### make the input-list for the writeCdf-function
  if(verbose)
cat(paste("Creating CDF list for", nunits, "units.\n"))
  newCdfList <- lapply(ffs, pmFeature2List)

  ### writing the cdf-file (binary-file)
  writeCdf(newCdfHeader$filename, cdfheader= newCdfHeader, cdf=newCdfList, 
cdfqc=NULL, verbose=verbose, overwrite=overwrite)

}


> sessionInfo()
R version 2.10.1 (2009-12-14) 
x86_64-unknown-linux-gnu 

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C  
 [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C  LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8   LC_NAME=C 
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C   

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

other attached packages:
 [1] makecdfenv_1.24.0 affyio_1.14.0
 [3] affy_1.24.2   pdInfoBuilder_1.10.1 
 [5] affxparser_1.18.0 pd.hugene.1.0.st.v1_3.0.0
 [7] RSQLite_0.8-0 DBI_0.2-5
 [9] oligo_1.10.0  preprocessCore_1.8.0 
[11] oligoClasses_1.8.0Biobase_2.6.1

loaded via a namespace (and not attached):
[1] Biostrings_2.14.10 IRanges_1.4.9  splines_2.10.1 tools_2.10.1  
> 

 
Guido Hooiveld, PhD 
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition 
Wageningen University 
Biotechnion, Bomenweg 2 
NL-6703 HD Wageningen 
the Netherlands 
tel: (+)31 317 485788 
fax: (+)31 317 483342 
internet:   http://nutrigene.4t.com
email:  guido.hooiv...@wur.nl

 

> -Original Message-
> From: Mark Robinson [mailto:mrobin...@wehi.edu.au] 
> Sent: 20 April 2010 00:34
> To: Hooiveld, Guido
> Subject: Re: PdInfo2Cdf function
> 
> Hi Guido.
> 
> A quick response that might help get you rolling.  The 
> challenging thing about all this is that the underlying 
> packages (e.g. pdInfoBuilder) change all the time and its 
> hard to keep up.  I haven't had any experience with the Gene 
> 1.1 arrays, but assuming you know a bit of R, what would be 
> good to do is

RE: [aroma.affymetrix] AffymetrixCdfFile$byChipType -- Argument 'nbrOfUnits' contains 1 NA value(s)

RE: [aroma.affymetrix] Construct cdf file from pgf, clf and gene mapping file

RE: [aroma.affymetrix] gene-centric CDF for HT HG U133A arrays (TCGA GBM data)

RE: [aroma.affymetrix] CDF file for Human Gene 1.1 st array

RE: [aroma.affymetrix] Re: Gene 2.0 ST arrays

RE: [aroma.affymetrix] Re: Gene 2.0 ST arrays

[aroma.affymetrix] binary CDF files on-line

RE: [aroma.affymetrix] Affymetrix Gene 2.0 ST-array cdf files for Human, Mouse and rat.

[aroma.affymetrix] Error in if (hasTimestamp) { : argument is of length zero

RE: [aroma.affymetrix] Gene 2.0 ST arrays

RE: [aroma.affymetrix] Gene 2.0 ST arrays

RE: [aroma.affymetrix] aroma.affymetrix v2.1.0 released

RE: [aroma.affymetrix] Re: writeCdf.AffyGenePDInfo Error in order(u$atom): argument 1 is not a vector

[aroma.affymetrix] bug in function pdInfo2Cdf

[aroma.affymetrix] RE: PdInfo2Cdf function

[aroma.affymetrix] RE: PdInfo2Cdf function

[aroma.affymetrix] RE: PdInfo2Cdf function

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