[BioC] xps: root scheme annotations

cstrato cstrato at aon.at
Wed Aug 24 23:30:15 CEST 2011

Dear Ed,

Please note that vignette xps.pdf handles mainly expression arrays (with 
Test3 as an example), however, Appendix A mentions:
"Package xps includes a file ”script4schemes.R”,..."

Please have a look at ”script4schemes.R” which is located in the 
xps/examples directory. It does contain the code to create schemes for 
many arrays, including MoGene arrays.
You could also get ”script4schemes.R” from the development version of 
xps, since this does already contain the code for the annotation version 
na32 which Affymetrix has just released. (Please ignore the Warnings 
which I forgot to delete.)

Best regards
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at

On 8/24/11 10:30 PM, Ed Siefker wrote:
> 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
> MoGene-1_0-st-v1.na31.mm9.transcript.csv.
> 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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