Hi Steven,

I think this may be related to a problem that was raised on the Bioc-devel
mailing list a couple of months ago:

https://stat.ethz.ch/pipermail/bioc-devel/2011-November/002955.html

If indeed it's the same issue then the discussion above indicates it was
patch from affy version 1.33.1

Mike

On Tue, Jan 24, 2012 at 1:07 PM, Osselaer, Steven [JRDBE Extern] <
SOSSELAE@its.jnj.com> wrote:

> 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@r-project.org
> [mailto:bioconductor-bounces@r-project.org] On Behalf Of Wolfgang Huber
> Sent: Tuesday, 24 January 2012 13:59
> To: bioconductor@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.
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@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
>
> _______________________________________________
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> Bioconductor@r-project.org
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> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
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>



-- 
Mike Smith
PhD Student
Computational Biology Group
Cambridge University

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