[BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips
Benilton Carvalho
beniltoncarvalho at gmail.com
Tue Jan 24 16:53:23 CET 2012
Also, feel free to ping me (via mailing list is preferred, as others
may benefit as well; but i don't mind direct emails if needed) re:
issues/suggestions/questions about oligo. b
On 24 January 2012 14:21, Osselaer, Steven [JRDBE Extern]
<SOSSELAE at its.jnj.com> wrote:
> 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.
>>>
>>> _______________________________________________
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>> 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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>>
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>>
>>
>>
>>
>>
>>
>>
>
> --
> 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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