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

James W. MacDonald jmacdon at med.umich.edu
Thu Nov 10 15:28:10 CET 2011


Hi Tim,

There were two attempts to modify read.affybatch() to work with 
non-square arrays, and neither involved the change you suggest. Anyway, 
your change doesn't materially affect how read.affybatch() works for the 
intended 3' biased arrays, so I have made the change.

This is in svn now, and will be propagated to the devel version (1.33.1) 
in 24 hours or so.

Best,

Jim

On 11/10/2011 6:45 AM, Tim Rayner wrote:
> 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.
>
> Cheers,
>
> Tim
>
> 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)
>> $NROW
>> [1] 1050
>>
>> $NCOL
>> [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
>>
>> **********************************************************
>> 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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-- 
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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