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

Fri, Nov 4, 2011 6:04 AM #

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.

Best regards,

Tim Rayner

Bioinformatician
Smith Lab, CIMR
University of Cambridge





Index: R/read.affybatch.R
===================================================================
--- R/read.affybatch.R	(revision 60068)
+++ R/read.affybatch.R	(working copy)
@@ -100,7 +100,7 @@

   exprs <- .Call("read_abatch",filenames, rm.mask,
                rm.outliers, rm.extra, ref.cdfName,
-               dim.intensity[c("Rows","Cols")],verbose, PACKAGE="affyio")
+               dim.intensity[c(1,2)],verbose, PACKAGE="affyio")
   colnames(exprs) <- samplenames

   #### this is where the code changes from the original read.affybatch.

James W. MacDonald

Wed, Nov 9, 2011 2:45 PM #

Hi Tim,

On 11/4/2011 9:04 AM, Tim Rayner wrote:

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

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

Thu, Nov 10, 2011 3:01 AM #

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