Hi Jim,

Tim mentioned that he was using the GeneST plates, which, rather than
chips.  As far as I'm aware these were all given the version number 1.1 by
Affy. If you run your code on the Mouse v1.1 it doesn't come back as square.

> suppressMessages(library(pd.mogene.1.1.st.v1))
> con <- db(pd.mogene.1.1.st.v1)
> max(dbGetQuery(con, "select x from pmfeature;"))
[1] 989
> max(dbGetQuery(con, "select y from pmfeature;"))
[1] 1189

Cheers,

Mike

On Wed, Nov 9, 2011 at 10:45 PM, James W. MacDonald
<jmacdon@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
>
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-- 
Mike Smith
PhD Student
Computational Biology Group
Cambridge University

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