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

Osselaer, Steven [JRDBE Extern] SOSSELAE at ITS.JNJ.COM
Tue Jan 24 15:21:57 CET 2012


Thank you for this information, James.
We will look into this and try start using 'oligo' for these types of
arrays.

Kind regards,
Steven

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Tuesday, 24 January 2012 15:18
To: Osselaer, Steven [JRDBE Extern]
Cc: Mike Smith; bioconductor at r-project.org
Subject: Re: [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips

Hi Steven,

If you follow the discussion that Mike linked to, this has been 
corrected in the devel version of the affy package. I made this change 
because it didn't have an adverse effect on the intended target of the 
affy package, which is the 3' biased arrays. I have not made the change 
in the release version because it isn't a bug.

I also made this change because people seem to want to use the affy 
package for analyzing the Gene ST chips even though it was never 
intended for this purpose, and doesn't really do a good job. The oligo 
package is intended to be used with these chips, and that is the package

we recommend you use.

I think some of the hesitation to use oligo stems from the fact that it 
had a long development cycle, and in earlier incarnations was not 
completely documented. This is no longer true, and I would recommend you

at least take a look.

Best,

Jim



On 1/24/2012 9:01 AM, Osselaer, Steven [JRDBE Extern] wrote:
> Thanks a lot, Mike.
>
> Applying the patch makes the ReadAffy() call functional again for
these
> types of chips.
>
>
>
> Kind regards,
>
> Steven Osselaer
>
>
>
> From: Mike Smith [mailto:grimbough at gmail.com]
> Sent: Tuesday, 24 January 2012 14:30
> To: Osselaer, Steven [JRDBE Extern]
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips
>
>
>
> 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 at 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 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.
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
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>> 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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
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> Search the archives:
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>
> _______________________________________________
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> Bioconductor at r-project.org
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> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>
>
>
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826

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