[BioC] xps: root scheme annotations

Ed Siefker ebs15242 at creighton.edu
Wed Aug 24 22:30:58 CEST 2011

I am trying to analyze data from Affymetrix Mouse Gene 1.0 ST arrays.
I am using the 'xps' package as recommended by this list. I compiled
and installed root successfully, and was able to install xps.

I am now trying to follow the instructions in Appendix A of xps.pdf.
My problem is finding the right annotations file. Here is the error
when I try to build the scheme file:
> Error in import.expr.scheme("Scheme_mRNA", filedir = scmdir, 
> paste(libdir, :
> ‘annotfile’ does not end with ‘annot.csv’

Affymetrix distributes 2 annotation files for these chips,
MoGene-1_0-st-v1.na31.mm9.probeset.csv and

Neither of these end in 'annot.csv'. Should I rename one of them
to end in annot.csv? Which one? Or should I just cat them both
into 'annot.csv'? Am I using the wrong files entirely? Where can
I get the proper file?

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