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

[Wolfgang Huber]

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.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
Best wishes
	Wolfgang

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