[Bioc-devel] affy package and non-square arrays

Tim Rayner tfrayner at gmail.com
Thu Nov 10 12:45:03 CET 2011

Sorry, I apparently hit 'reply' instead of 'reply all'. Forwarding
back to the list:

---------- Forwarded message ----------
From: Tim Rayner <tfrayner at gmail.com>
Date: 10 November 2011 10:08
Subject: Re: [Bioc-devel] affy package and non-square arrays
To: "James W. MacDonald" <jmacdon at med.umich.edu>

Hi Jim,

The problem lies with the GeneTitan (a.k.a. 'plate', e.g. HuGene-1.1)
versions of these arrays, which are decidedly non-square (1190 x 990).
We have our own CDF packages which support these arrays and which have
been working with the read.affybatch function for well over a year,
which is why I suspected that recent changes in the affy package might
be responsible. The original error message was:

> ReadAffy('GSM737553_Sample_1.CEL.CEL', cdfname='hugene10stsl')
Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData,  :
 Cel file GSM737553_Sample_1.CEL.CEL does not seem to have the
correct dimensions

See http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM737553 for an
example of this type of array; a suitable custom CDF for testing would
be http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.1.0/entrezg.download/hugene11stv1hsentrezgcdf_14.1.0.tar.gz

I'm reasonably sure I saw a recent release version of the package
installed on one of our machines which had this bug fixed, but it
seems to have been overwritten with the original version sometime in
the last 48 hours.

I understand that the affy package is not the recommended analysis
platform for GeneST chips; we are (slowly) transitioning to using the
oligo package for all new work but I figured you'd still like to know
of problems such as this.



On 9 November 2011 22:45, James W. MacDonald <jmacdon at med.umich.edu> wrote:
> Hi Tim,
> On 11/4/2011 9:04 AM, Tim Rayner wrote:
>> Hi,
>> The latest release version of the affy package (v.1.32.0) seems to
>> have introduced a bug in the ReadAffy function which prevents it from
>> reading data from non-square arrays (e.g. the GeneST array plates).
>> Looking back at an earlier, related SVN commit (50736), it appears
>> that the attached patch should fix the bug. I've tested this on my
>> Bioc 2.9 installation and it gives the expected results.
> Can you elaborate on this please? What Gene ST array are you using, and what
> happens when you try to read it in? I have tested both mouse and rat Gene ST
> data using the current BioC, and don't have any problems.
> As an aside, I don't see any indication that these arrays are non-square:
>> library(hugene10stv1cdf)
>> as.list(hugene10stv1dim)
> [1] 1050
> [1] 1050
> But maybe the cdf packages are not correct, let's try the
> pd.hugene.1.0.st.v1.
>> suppressMessages(library(pd.hugene.1.0.st.v1))
>> con <- db(pd.hugene.1.0.st.v1)
>> max(dbGetQuery(con, "select x from pmfeature;"))
> [1] 1048
>> max(dbGetQuery(con, "select y from pmfeature;"))
> [1] 1048
> Best,
> Jim
>> Best regards,
>> Tim Rayner
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
> **********************************************************
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