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?

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 Christian _._._._._._._._._._._._._._._._._._ 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? > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >