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

[James W. MacDonald]

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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