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

Tim Rayner tfrayner at gmail.com
Fri Nov 4 14:04:39 CET 2011


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

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.

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