[BioC] affy : ReadAffy() fails on HuGene-1_1-st-v1 chips
James W. MacDonald
jmacdon at med.umich.edu
Mon Jan 30 16:53:50 CET 2012
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 at 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 at 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 at 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 at wur.nl
>>>>>> I: http://humannutrition.wur.nl
>>>>>> https://madmax.bioinformatics.nl
>>>>>> http://www.nutrigenomicsconsortium.nl
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: James W. MacDonald [mailto:jmacdon at med.umich.edu]
>>>>>> Sent: donderdag 26 januari 2012 15:32
>>>>>> To: Groot, Philip de
>>>>>> Cc: 'Osselaer, Steven [JRDBE Extern]'; Goehlmann, Hinrich [JRDBE];
>>>>>> bioconductor at 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 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.
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Bioconductor mailing list
>>>>>>>>> Bioconductor at 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 at 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 at 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 at 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 at 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 at 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
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