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List: bioconductor
Subject: Re: [BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips
From: "James W. MacDonald" <jmacdon () med ! umich ! edu>
Date: 2012-01-30 15:53:50
Message-ID: 4F26BD0E.4080608 () med ! umich ! edu
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I forgot to mention that I have made these changes to both devel and
release (so the release version will now process non-square arrays
correctly), and that AFAICT these changes don't break anything.
I still think there is something weird here, as the dimensions reported
are not correct; the array is wider than it is tall, and affy reports
the opposite. But whatever...
Best,
Jim
On 1/30/2012 10:21 AM, James W. MacDonald wrote:
> Hi Ben,
>
> Thanks for testing. I agree about the weird annotation, but it doesn't
> come from name indexing.
>
> The changes you and Kasper made are here (note this is the current
> code, and the changes you made in Nov 2010 are extant in both release
> and devel):
>
> return(new("AffyBatch",
> exprs = exprs,
> se.exprs = .Call("read_abatch_stddev",filenames, rm.mask,
> rm.outliers, rm.extra, ref.cdfName,
> dim.intensity,verbose, PACKAGE="affyio"),
> cdfName = cdfname, ##cel@cdfName,
> phenoData = phenoData,
> nrow = dim.intensity[1],##["Rows"],
> ncol = dim.intensity[2],##["Cols"],
> annotation = cleancdfname(cdfname, addcdf=FALSE),
> protocolData = protocol,
> description= description,
> notes = notes))
>
> The change I made is
>
> exprs <- .Call("read_abatch",filenames, rm.mask,
> rm.outliers, rm.extra, ref.cdfName,
> dim.intensity[c(1,2)],verbose, PACKAGE="affyio")
>
> where originally the dim.intensity was indexed by c("Row","Col").
>
> If we debug() read.affybatch(), we get this:
>
> headdetails
> $cdfName
> [1] "HuGene-1_1-st-v1"
>
> $`CEL dimensions`
> Cols Rows
> 990 1190
>
> Which indicates to me that perhaps when instantiating the AffyBatch,
> ncol should be dim.intensity[1], and nrow should be dim.intensity[2],
> or the opposite of the current code.
>
> An example with these same HuGene 1.1 ST arrays:
>
> > dat
> AffyBatch object
> size of arrays=1190x990 features (17 kb)
> cdf=HuGene-1_1-st-v1 (33297 affyids)
> number of samples=2
> number of genes=33297
> annotation=hugene11stv1
> notes=
> > nrow(dat)
> Rows
> 1190
> > ncol(dat)
> Cols
> 990
> > dim(dat)
> Rows Cols
> 1190 990
> > sessionInfo()
> R Under development (unstable) (2011-08-04 r56624)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915
> [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] hgfocuscdf_2.8.0 hugene11stv1cdf_2.4.0 AnnotationDbi_1.15.10
> [4] affyPLM_1.29.2 preprocessCore_1.15.0 gcrma_2.25.2
> [7] affy_1.32.1 Biobase_2.13.7
>
> loaded via a namespace (and not attached):
> [1] affyio_1.21.2 BiocInstaller_1.2.1 Biostrings_2.21.9
> [4] DBI_0.2-5 IRanges_1.11.24 RSQLite_0.9-4
> [7] splines_2.14.0 tools_2.14.0 zlibbioc_0.1.7
> >
>
> Best,
>
> Jim
>
>
> On 1/28/2012 9:21 PM, Ben Bolstad wrote:
> > Hi Jim,
> >
> > Grabbing some data from GEO and testing, as far as I can tell the
> > current affy 1.33.2 image() command is fine for HuGene 1.1 st, at
> > least if you use the brainarray cdfenv.
> >
> > Similarly the affyPLM images look correctly oriented etc.
> >
> > One note, ncol() and nrow() on an AffyBatch object do look weirdly
> > annotated in this context (one of the reasons I fought with the use
> > of name indexing in my patch downthread).
> >
> > In any case, I don't see why the release branch could not be patched
> > with this bug fix besides the strong coercive effects already
> > discussed below. But then again, I'm not eating my own dog food much
> > these days, so I'm not going to attempt it myself lest I make things
> > worse.
> >
> > Best,
> >
> > Ben
> >
> >
> > > Data<-
> > > ReadAffy("GSM801200_G032A_A09_3_JGRA2_P1.CEL.gz","GSM801203_G032A_B09_6_JNIX4_P2.CEL.gz",cdfname="hugene11stv1hsentrezgcdf")
> > > Data
> > AffyBatch object
> > size of arrays=990x1190 features (17 kb)
> > cdf=hugene11stv1hsentrezgcdf (19738 affyids)
> > number of samples=2
> > number of genes=19738
> > annotation=hugene11stv1hsentrezgcdf
> > notes=
> > > nrow(Data)
> > Cols
> > 990
> > > ncol(Data)
> > Rows
> > 1190
> > > dim(data)
> > NULL
> > > dim(Data)
> > Cols Rows
> > 990 1190
> > > 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] hugene11stv1hsentrezgcdf_14.1.0 affyPLM_1.30.0
> > [3] preprocessCore_1.16.0 gcrma_2.26.0
> > [5] affy_1.33.2 Biobase_2.14.0
> > [7] BiocGenerics_0.1.4
> >
> > loaded via a namespace (and not attached):
> > [1] affyio_1.22.0 BiocInstaller_1.2.1 Biostrings_2.22.0
> > [4] IRanges_1.12.5 splines_2.14.1 tools_2.14.1
> > [7] zlibbioc_1.0.0
> >
> >
> > On Fri, 2012-01-27 at 13:32 -0500, James W. MacDonald wrote:
> > > Hi Ben,
> > >
> > > I can't find anything in the archives corresponding to images being
> > > wrong. The only two threads I can find are these:
> > >
> > > https://stat.ethz.ch/pipermail/bioc-devel/2010-May/002209.html
> > > https://stat.ethz.ch/pipermail/bioc-devel/2010-April/002177.html
> > >
> > > But I wonder if there is still a problem.
> > >
> > > Will someone who has GeneTitan data please use either the devel (or
> > > self-patched) version of affy to read in some chips, use fitPLM() in
> > > affyPLM to summarize, and then see if the image() function works
> > > correctly?
> > >
> > > Best,
> > >
> > > Jim
> > >
> > >
> > >
> > > On 1/27/2012 11:39 AM, Ben Bolstad wrote:
> > > > I probably should not be responding, lest I say something stupid
> > > > (though I agree that I am highly imperfect). Plus, I am away from both
> > > > my email archives and any sort of machine that I can use to test
> > > > things out which only exacerbates the chances of incorrectness.
> > > >
> > > > However, any changes that I made were most probably in response to an
> > > > urgent user request to "make things work now". My vague recollections
> > > > are something to do with making chip images, probably of the affyPLM
> > > > variety (though perhaps image() on an AffyBatch as well) correct.
> > > >
> > > > In any case read.affybatch() calls the parser in affyio. The parser in
> > > > affyio returns the chip dimensions in the order in which they are read
> > > > from the CEL file. According to the documentation that Affymetrix
> > > > places on their website (the documentation used to write the parser,
> > > > at least past the point at which it was no longer reverse engineered
> > > > from the old text CEL format) "Columns" are reported before "Rows" in
> > > > the text and xda CEL formats (not to sure about generic "calvin"
> > > > format right this minute). Based on that convention the function has
> > > > always returned them in that order (though I agree this is
> > > > non-conventional).
> > > >
> > > > It may be that CEL file "Rows" and "Columns" are sometimes transposed
> > > > relative to CDF file "Rows" and "Columns" (and to make things worse
> > > > Cols came before Rows in the text version of the CDF file, and Rows
> > > > before Columns in the XDA CDF format). I don't recall off the top of
> > > > my head whether the parser used by makecdfenv honors this properly.
> > > >
> > > >
> > > > Ben
> > > >
> > > >
> > > > On 27.01.2012 07:28, James W. MacDonald wrote:
> > > > > Hi Philip,
> > > > >
> > > > > On 1/27/2012 3:18 AM, Groot, Philip de wrote:
> > > > > > 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!
> > > > > I am happy to hear that. Benilton has invested untold hours
> > > > > developing oligo/pdInfoBuilder, and he deserves the appreciation.
> > > > >
> > > > > > 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."
> > > > > The definition of a bug is when software doesn't do something that
> > > > > the author intends it to do. I and others have stated numerous times
> > > > > that the affy package is not and never was intended for use with any
> > > > > chip type but the 3'-biased chips. You could just as easily declare
> > > > > that is a bug that affy won't process SNP chips, and it would make as
> > > > > much sense.
> > > > >
> > > > > > 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...
> > > > > First you apologize, and then you insult...
> > > > >
> > > > > Here again your ignorance of the process has caused you to stray into
> > > > > dangerous lands. It seems to me you want to assume treachery or
> > > > > collusion when the most likely cause is well-intentioned error. To
> > > > > disabuse you of this notion, let's look at the svn logs, shall we?
> > > > >
> > > > > In May 2010, Kasper Daniel Hansen made some changes:
> > > > >
> > > > > svn log -r 47059
> > > > >
> > > > > ------------------------------------------------------------------------
> > > > >
> > > > > r47059 | khansen | 2010-05-20 20:21:16 -0400 (Thu, 20 May 2010) |
> > > > > 1 line
> > > > >
> > > > > Uses names from the output of read.celfile.header in read.affybatch;
> > > > > recent addition to affyio. This fixes a bug in read.affybatch having
> > > > > to do with non-square arrays
> > > > >
> > > > > ------------------------------------------------------------------------
> > > > >
> > > > >
> > > > > The changes he made:
> > > > >
> > > > > svn diff -r 47060:47050 read.affybatch.R
> > > > > Index: read.affybatch.R
> > > > > ===================================================================
> > > > > --- read.affybatch.R (revision 47060)
> > > > > +++ read.affybatch.R (revision 47050)
> > > > > @@ -111,8 +111,8 @@
> > > > > ##se.exprs = array(NaN, dim=dim.sd),
> > > > > cdfName = cdfname, ##cel@cdfName,
> > > > > phenoData = phenoData,
> > > > > - nrow = dim.intensity["Rows"],
> > > > > - ncol = dim.intensity["Cols"],
> > > > > + nrow = dim.intensity[1],
> > > > > + ncol = dim.intensity[2],
> > > > > annotation = cleancdfname(cdfname, addcdf=FALSE),
> > > > > protocolData = protocol,
> > > > > description= description,
> > > > >
> > > > > Changing the subsetting of dim.intensity to use "Rows" and "Cols"
> > > > > rather than 1/2.
> > > > >
> > > > > In November 2010, Ben Bolstad made some changes:
> > > > >
> > > > > svn log -r 50736
> > > > >
> > > > > ------------------------------------------------------------------------
> > > > >
> > > > > r50736 | bolstad | 2010-11-07 00:48:33 -0400 (Sun, 07 Nov 2010) | 2
> > > > > lines
> > > > >
> > > > > fixes to handle non square arrays
> > > > >
> > > > >
> > > > > ------------------------------------------------------------------------
> > > > >
> > > > >
> > > > >
> > > > > The changes he made were
> > > > >
> > > > > svn diff -r 50730:50740 read.affybatch.R
> > > > > Index: read.affybatch.R
> > > > > ===================================================================
> > > > > --- read.affybatch.R (revision 50730)
> > > > > +++ read.affybatch.R (revision 50740)
> > > > > @@ -111,8 +111,8 @@
> > > > > ##se.exprs = array(NaN, dim=dim.sd),
> > > > > cdfName = cdfname, ##cel@cdfName,
> > > > > phenoData = phenoData,
> > > > > - nrow = dim.intensity["Rows"],
> > > > > - ncol = dim.intensity["Cols"],
> > > > > + nrow = dim.intensity[1],##["Rows"],
> > > > > + ncol = dim.intensity[2],##["Cols"],
> > > > > annotation = cleancdfname(cdfname, addcdf=FALSE),
> > > > > protocolData = protocol,
> > > > > description= description,
> > > > >
> > > > > Where he changed the code back to the original version.
> > > > >
> > > > > Then in November 2011, yours truly made some changes:
> > > > >
> > > > > svn log -r 60183
> > > > >
> > > > > ------------------------------------------------------------------------
> > > > >
> > > > > r60183 | jmacdon | 2011-11-10 09:24:59 -0500 (Thu, 10 Nov 2011) |
> > > > > 1 line
> > > > >
> > > > > Modifications to read.affybatch() to allow reading of non-square
> > > > > arrays
> > > > >
> > > > > ------------------------------------------------------------------------
> > > > >
> > > > >
> > > > > And those changes were
> > > > >
> > > > > svn diff -r 60185:60180 read.affybatch.R
> > > > > Index: read.affybatch.R
> > > > > ===================================================================
> > > > > --- read.affybatch.R (revision 60185)
> > > > > +++ read.affybatch.R (revision 60180)
> > > > > @@ -100,7 +100,7 @@
> > > > >
> > > > > exprs<- .Call("read_abatch",filenames, rm.mask,
> > > > > rm.outliers, rm.extra, ref.cdfName,
> > > > > - dim.intensity[c(1,2)],verbose, PACKAGE="affyio")
> > > > > + dim.intensity[c("Rows","Cols")],verbose,
> > > > > PACKAGE="affyio")
> > > > > colnames(exprs)<- samplenames
> > > > >
> > > > > where we go back to subsetting dim.intensity by "Row" and "Col".
> > > > >
> > > > >
> > > > > Here we have three instances of three different people trying to make
> > > > > sure the affy package will work with the non-square arrays. One
> > > > > attempt had the unintended effect of unfixing a previous fix. This is
> > > > > unfortunate, but given the imperfection of the human species, and the
> > > > > fact that multiple people have write access for this package,
> > > > > mistakes
> > > > > will be made.
> > > > >
> > > > > There is, however, no evidence of capriciousness nor ill will towards
> > > > > those unlucky souls trying to analyze non-square arrays with the affy
> > > > > package.
> > > > >
> > > > >
> > > > > > 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 appr!
> > > > > ec!
> > > > > > iated.
> > > > > I see, you are trying to help. Good for you. I wonder exactly what
> > > > > you are doing other than complaining bitterly about honest mistakes
> > > > > and casting aspersions on people whom you seem to think have done you
> > > > > harm. What ever it is, keep up the good work.
> > > > >
> > > > > Best,
> > > > >
> > > > > Jim
> > > > > > 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
> > > > > >
> > > > > > _______________________________________________
> > > > > > 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
> > > > >
> > > > > _______________________________________________
> > > > > 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
_______________________________________________
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
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