As many users know xps supports the whole genome arrays HuGene, MoGene and RaGene, both release r3 and release r4. While xps works with HuGene arrays as expected some users have currently reported problems with MoGene arrays. The reason is that Affymetrix has just updated the PGF-files for the MoGene and RaGene arrays by deleting an AFFX control probeset which was causing an error in APT when using the option "-a dabg" (see the corresponding README files). However, at the moment Affymetrix has not deleted this probeset from the corresponding transcript and probset annotation files, which causes an error in xps since it checks for consistency between these files. Affymetrix has already promised to update the annotation files in the next release of the files. Meanwhile, I need to ask the users of xps to use the following function to update the annotation files for the MoGene and RaGene arrays: "updateAnnotation" <- function(infile, outfile, probeset, skip, eol="\n") { ## read header and probesets cat("reading", infile, "...\n"); header <- readLines(infile, n=skip); annot <- read.csv(infile, colClasses="character", comment.char="", skip=skip); ## delete probeset line <- which(annot[,"probeset_id"] == probeset); if (length(line) > 0) { cat("deleting line", line, "for probeset", probeset, "...\n"); annot <- annot[-line,]; }#if ## write header and append probesets ## (use binary file to prevent conversion of LF to CRLF on WinXP) cat("writing", outfile, "...\n"); file <- file(outfile, "wb") writeLines(header, con=file, sep=eol); write.table(annot, file=file, append=TRUE, sep=",", eol=eol, row.names=FALSE); close(file) }#updateAnnotation For MoGene arrays please use the following code to update the annotation files: # probeset annotation updateAnnotation("MoGene-1_0-st-v1.na29.mm9.probeset.csv", "MoGene-1_0-st-v1.na29.mm9.probeset.fixed.csv", probeset="10338063", skip=18, eol="\n") # transcript annotation updateAnnotation("MoGene-1_0-st-v1.na29.mm9.transcript.csv", "MoGene-1_0-st-v1.na29.mm9.transcript.fixed.csv", probeset="10338063", skip=19, eol="\n") You can then create the scheme for MoGene as follows: scheme.mogene10stv1r4.na29 <- import.exon.scheme("Scheme_MoGene10stv1r4_na29",filedir=scmdir, paste(libdir,"MoGene-1_0-st-v1.r4.analysis-lib-files/MoGene- 1_0-st-v1.r4.clf",sep="/"), paste(libdir,"MoGene-1_0-st-v1.r4.analysis-lib-files/MoGene- 1_0-st-v1.r4.pgf",sep="/"), paste(anndir,"MoGene-1_0-st-v1.na29.mm9.probeset.fixed.csv",sep="/"), paste(anndir,"MoGene- 1_0-st-v1.na29.mm9.transcript.fixed.csv",sep="/")) For RaGene arrays please use the following code to update the annotation files: # probeset annotation updateAnnotation("RaGene-1_0-st-v1.na29.rn4.probeset.csv", "RaGene-1_0-st-v1.na29.rn4.probeset.fixed.csv", probeset="10700063", skip=18, eol="\n") # transcript annotation updateAnnotation("RaGene-1_0-st-v1.na29.rn4.transcript.csv", "RaGene-1_0-st-v1.na29.rn4.transcript.fixed.csv", probeset="10700063", skip=19, eol="\n") You can then create the scheme for RaGene as follows: scheme.ragene10stv1r4.na29 <- import.exon.scheme("Scheme_RaGene10stv1r4_na29",filedir=scmdir, paste(libdir,"RaGene-1_0-st-v1.r4.analysis-lib-files/RaGene- 1_0-st-v1.r4.clf",sep="/"), paste(libdir,"RaGene-1_0-st-v1.r4.analysis-lib-files/RaGene- 1_0-st-v1.r4.pgf",sep="/"), paste(anndir,"RaGene-1_0-st-v1.na29.rn4.probeset.fixed.csv",sep="/"), paste(anndir,"RaGene- 1_0-st-v1.na29.rn4.transcript.fixed.csv",sep="/")) Please feel free to ask me if you have any further questions. 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 _._._._._._._._._._._._._._._._._._