[BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips
Groot, Philip de
philip.degroot at wur.nl
Thu Jan 26 10:28:05 CET 2012
Hello all,
Just to be sure:
>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 think it is not nice that the problem will reoccur everytime a new release is present? So I do hope that the patch is included in the next Bioconductor release? Please acknowledge!
In addition, I severely tested affy and oligo RMA normalization using either the CDF (http://nmg-r.bioinformatics.nl/NuGO_R.html) or the pd.mapping (Bioconductor oligo) libraries. The RMA results are identical upon to last digit!
In conclusion: it works in both ways, so let's support it properly then! Note: I do agree that the oligo package is better suited for handling 3rd generation Affymetrix arrays, but intentionally sabotaging the affy library ((sorry, but it just looks like this) is not the way to force people to move to oligo. Just my 2 cents.
Regards,
Dr. Philip de Groot
Bioinformatician / Microarray analysis expert
Wageningen University / TIFN
Netherlands Nutrigenomics Center (NNC)
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
PO Box 8129, 6700 EV Wageningen
Visiting Address:
"De Valk" ("Erfelijkheidsleer"),
Building 304,
Verbindingsweg 4, 6703 HC Wageningen
Room: 0052a
T: 0317 485786
F: 0317 483342
E-mail: Philip.deGroot at wur.nl
I: http://humannutrition.wur.nl
https://madmax.bioinformatics.nl
http://www.nutrigenomicsconsortium.nl
-----Original Message-----
From: Osselaer, Steven [JRDBE Extern] [mailto:SOSSELAE at ITS.JNJ.COM]
Sent: dinsdag 24 januari 2012 15:22
To: James W. MacDonald
Cc: Goehlmann, Hinrich [JRDBE]; bioconductor at r-project.org
Subject: Re: [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips
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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