[BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips

Osselaer, Steven [JRDBE Extern] SOSSELAE at ITS.JNJ.COM
Tue Jan 24 14:07:46 CET 2012 

Dear Wolfgang,

I was under the impression that it was a problem with the software as I
can read the same CEL files with the R 2.13.1 software : see transcript
for the same code but run under R 2.13.1 below.

Kind regards,
Steven

R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(affy)
Loading required package: Biobase

Welcome to Bioconductor

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

> sessionInfo()
R version 2.13.1 (2011-07-08)
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-8        LC_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] affy_1.30.0    Biobase_2.12.2

loaded via a namespace (and not attached):
[1] affyio_1.20.0         preprocessCore_1.14.0
> celFiles <- list.files(pattern="CEL$")
> celFiles
 [1] "27002.CEL" "27003.CEL" "27004.CEL" "27005.CEL" "27006.CEL"
"27007.CEL"
 [7] "27008.CEL" "27009.CEL" "27010.CEL" "27011.CEL" "27012.CEL"
"27013.CEL"
[13] "27014.CEL" "27015.CEL" "27016.CEL" "27017.CEL" "27018.CEL"
"27019.CEL"
[19] "27020.CEL" "27021.CEL" "27022.CEL" "27023.CEL" "27024.CEL"
"27025.CEL"
[25] "27026.CEL" "27027.CEL" "27028.CEL" "27029.CEL" "27030.CEL"
"27031.CEL"
[31] "27032.CEL" "27033.CEL" "27034.CEL" "27035.CEL" "27036.CEL"
"27037.CEL"
[37] "27038.CEL" "27039.CEL" "27040.CEL" "27041.CEL" "27042.CEL"
"27043.CEL"
[43] "27044.CEL" "27045.CEL" "27046.CEL" "27047.CEL" "27048.CEL"
"27049.CEL"
[49] "27050.CEL" "27051.CEL" "27052.CEL" "27053.CEL" "27054.CEL"
"27055.CEL"
[55] "27056.CEL" "27057.CEL" "27058.CEL" "27059.CEL" "27060.CEL"
"27061.CEL"
[61] "27062.CEL" "27063.CEL" "27064.CEL" "27065.CEL" "27066.CEL"
"27067.CEL"
[67] "27068.CEL" "27069.CEL" "27070.CEL" "27071.CEL" "27072.CEL"
"27073.CEL"
[73] "27074.CEL" "27075.CEL" "27076.CEL" "27077.CEL" "27078.CEL"
"27079.CEL"
[79] "27080.CEL" "27081.CEL" "27082.CEL" "27083.CEL" "27084.CEL"
"27085.CEL"
[85] "27086.CEL" "27087.CEL" "27088.CEL" "27089.CEL" "27090.CEL"
"27091.CEL"
[91] "27092.CEL" "27093.CEL" "27094.CEL" "27095.CEL" "27096.CEL"
> rawData <- ReadAffy(filenames=celFiles)
>
> q()


-----Original Message-----
From: bioconductor-bounces at r-project.org
[mailto:bioconductor-bounces at r-project.org] On Behalf Of Wolfgang Huber
Sent: Tuesday, 24 January 2012 13:59
To: bioconductor at r-project.org
Subject: Re: [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips


Dear Steven

thank you. What is your question, or why and how do you think someone 
other than the party who gave you the apparently faulty CEL file can 
help you?

	Best wishes
	Wolfgang




Steven Osselaer [guest] scripsit 01/24/2012 10:42 AM:
>
> Reading HuGene-1_1-st-v1 CEL files results in an error message about
incorrect dimensions of the first CEL file of the list
>
> TRANSCRIPT :
>
> R version 2.14.1 (2011-12-22)
> Copyright (C) 2011 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>    Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>> library(affy)
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
>    Vignettes contain introductory material. To view, type
>    'browseVignettes()'. To cite Bioconductor, see
>    'citation("Biobase")' and for packages 'citation("pkgname")'.
>
>> sessionInfo()
> R version 2.14.1 (2011-12-22)
> 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-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 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] affy_1.32.0    Biobase_2.14.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.22.0         BiocInstaller_1.2.1   preprocessCore_1.16.0
> [4] zlibbioc_1.0.0
>> celFiles<- list.files(pattern="CEL$")
>> celFiles
>   [1] "27002.CEL" "27003.CEL" "27004.CEL" "27005.CEL" "27006.CEL"
"27007.CEL"
>   [7] "27008.CEL" "27009.CEL" "27010.CEL" "27011.CEL" "27012.CEL"
"27013.CEL"
> [13] "27014.CEL" "27015.CEL" "27016.CEL" "27017.CEL" "27018.CEL"
"27019.CEL"
> [19] "27020.CEL" "27021.CEL" "27022.CEL" "27023.CEL" "27024.CEL"
"27025.CEL"
> [25] "27026.CEL" "27027.CEL" "27028.CEL" "27029.CEL" "27030.CEL"
"27031.CEL"
> [31] "27032.CEL" "27033.CEL" "27034.CEL" "27035.CEL" "27036.CEL"
"27037.CEL"
> [37] "27038.CEL" "27039.CEL" "27040.CEL" "27041.CEL" "27042.CEL"
"27043.CEL"
> [43] "27044.CEL" "27045.CEL" "27046.CEL" "27047.CEL" "27048.CEL"
"27049.CEL"
> [49] "27050.CEL" "27051.CEL" "27052.CEL" "27053.CEL" "27054.CEL"
"27055.CEL"
> [55] "27056.CEL" "27057.CEL" "27058.CEL" "27059.CEL" "27060.CEL"
"27061.CEL"
> [61] "27062.CEL" "27063.CEL" "27064.CEL" "27065.CEL" "27066.CEL"
"27067.CEL"
> [67] "27068.CEL" "27069.CEL" "27070.CEL" "27071.CEL" "27072.CEL"
"27073.CEL"
> [73] "27074.CEL" "27075.CEL" "27076.CEL" "27077.CEL" "27078.CEL"
"27079.CEL"
> [79] "27080.CEL" "27081.CEL" "27082.CEL" "27083.CEL" "27084.CEL"
"27085.CEL"
> [85] "27086.CEL" "27087.CEL" "27088.CEL" "27089.CEL" "27090.CEL"
"27091.CEL"
> [91] "27092.CEL" "27093.CEL" "27094.CEL" "27095.CEL" "27096.CEL"
>> rawData<- ReadAffy(filenames=celFiles)
> Error in read.affybatch(filenames = l$filenames, phenoData =
l$phenoData,  :
>    Cel file 27002.CEL does not seem to have the correct dimensions
>> traceback()
> 3: .Call("read_abatch", filenames, rm.mask, rm.outliers, rm.extra,
>         ref.cdfName, dim.intensity[c("Rows", "Cols")], verbose,
PACKAGE = "affyio")
> 2: read.affybatch(filenames = l$filenames, phenoData = l$phenoData,
>         description = l$description, notes = notes, compress =
compress,
>         rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra =
rm.extra,
>         verbose = verbose, sd = sd, cdfname = cdfname)
> 1: ReadAffy(filenames = celFiles)
>
>
>   -- output of sessionInfo():
>
> R version 2.14.1 (2011-12-22)
> 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-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 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] affy_1.32.0    Biobase_2.14.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.22.0         BiocInstaller_1.2.1   preprocessCore_1.16.0
> [4] zlibbioc_1.0.0
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber

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