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Subject: [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips
From: "Groot, Philip de" <philip.degroot () wur ! nl>
Date: 2012-01-27 8:18:20
Message-ID: 9C7DEC5AE512EE49931CB7437CAA61C626DA6173AC () scomp0536 ! wurnet ! nl
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Dear James,
I apologize for the email from yesterday. I totally agree with your points. In \
addition, I really appreciate the effort that is undertaken in establishing the oligo \
package. I am using the library myself regularly!
However, there is a reason why I reacted this way. The affy problem has been reported \
by me previously. And it was fixed in Bioconductor 2.8! Now it is broken again. Can \
happen, but this line really annoyed me:
(quote): " I have not made the change in the release version because it isn't a bug."
Definitely, it IS a bug. However, it does not affect analysis of Affymetrix arrays \
because the 1st and 2nd generation arrays are square. So you don't notice the problem \
and this is fine. This is also the reason why I am in doubt whether the fix will \
really stay in with the next release. It has been removed before without good \
reason...
In addition, people have invested some time to properly create CDF's for the \
geneTitan plates that do properly work with the affy library and provide (at least) \
identical RMA results with oligo. To my opinion, the great success and support of \
Bioconductor is for a significant part based on the affy library and the solutions \
that it offered when microarray analysis was at its infancy: it contributed in \
evolving Bioconductor to its current state! I think that the Bioconductor project \
should allow a "transitional period" where both affy and oligo can be utilized for \
analysing the most recent Affymetrix arrays. In addition, a lot of publications and \
tutorials are available that point people to the affy library and hence stimulate \
people to try it in the first place! Eventually, we should use oligo. No doubt about \
it, but the process should be a smooth transition. Currently, this is not the case. \
In addition, I am trying to help and I have the feeling that this is not well apprec! \
iated.
In summary: the oligo library has my full support, but I do hope that the affy-issue \
will be fixed because it is a good thing for the Bioconductor community.
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@wur.nl
I: http://humannutrition.wur.nl
https://madmax.bioinformatics.nl
http://www.nutrigenomicsconsortium.nl
-----Original Message-----
From: James W. MacDonald [mailto:jmacdon@med.umich.edu]
Sent: donderdag 26 januari 2012 15:32
To: Groot, Philip de
Cc: 'Osselaer, Steven [JRDBE Extern]'; Goehlmann, Hinrich [JRDBE]; \
bioconductor@r-project.org
Subject: Re: [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips
Hi Philip,
On 1/26/2012 4:28 AM, Groot, Philip de wrote:
> 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!
For those who don't understand how the BioC release cycle works, here is a short \
primer. At any one time there are two versions; the release version, which is \
considered to be stable, and the devel version, upon which developers are still \
working.
At each release the developers finish up all changes they have made to their \
packages, and the devel version is then split into a new release branch, which is \
then 'released'. This new release is then considered to be stable, and only bug fixes \
of sufficient gravity can be made. Since this patch doesn't fix a bug, it was not \
applied to the release version.
Therefore, by definition, all changes made to code in the devel version will make \
their way into the next release.
>
> 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.
That is a pretty harsh condemnation, and I will assume that you don't really mean it \
like it sounds, so I will try to show restraint.
A little background; several years ago it became clear that Affymetrix was going to \
have many more types of chips than just the original 3' biased chips for which the \
affy/makecdfenv pipeline was developed. After some discussion, Rafael Irizarry \
decided that rather than trying to reverse engineer an already existing and popular \
package to support all these new chips (in the six month span between releases), it \
would be better to create an entirely new pipeline that is intended to support ALL \
chips that Affy produces. The amount of time it took to get oligo/pdInfoBuilder to \
the current matured state is testament to the wisdom of that choice. Trying to 'fix' \
affy in six months would have been a disaster.
So, three points;
1.) Characterizing this as sabotage is (arrogant, ignorant, foolish, infuriating). I \
leave it to others to decide which. 2.) The affy and makecdfenv packages are open \
source. If you (or anybody else, for that matter) wants to fork the code into your \
own package that supports all and sundry, please feel free to do so. 3.) The original \
plan was for the affy package to be deprecated, and then removed from BioC. In \
deference to the vast user base who use this package, and the existing personal code \
that is based on affy, it was not deprecated. In addition, we have made changes where \
we can to make affy accomodate these new chips, even when it isn't in anybody's \
interest to do so. This, I believe, invalidates your accusation that people are being \
'forced to move to oligo'.
Best,
Jim
>
> 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@wur.nl
> I: http://humannutrition.wur.nl
> https://madmax.bioinformatics.nl
> http://www.nutrigenomicsconsortium.nl
>
>
>
> -----Original Message-----
> From: Osselaer, Steven [JRDBE Extern] [mailto:SOSSELAE@ITS.JNJ.COM]
> Sent: dinsdag 24 januari 2012 15:22
> To: James W. MacDonald
> Cc: Goehlmann, Hinrich [JRDBE]; bioconductor@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@med.umich.edu]
> Sent: Tuesday, 24 January 2012 15:18
> To: Osselaer, Steven [JRDBE Extern]
> Cc: Mike Smith; bioconductor@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@gmail.com]
> > Sent: Tuesday, 24 January 2012 14:30
> > To: Osselaer, Steven [JRDBE Extern]
> > Cc: bioconductor@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@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
> >
> > _______________________________________________
> > 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
> >
> > _______________________________________________
> > 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
> >
> >
> >
> >
> >
> >
> >
> --
> 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
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should
> not be used for urgent or sensitive issues
>
>
>
--
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
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for \
urgent or sensitive issues
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