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

[Steven Osselaer [guest]]

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)

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> 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


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