Dear list, I downloaded the three files (cdf, annotation, probes) from Affymetrix website; but I got the following error from using xps and mirna affymetrix annotation file. Warning: probeset <mml-mir-1224-star_st> has NumAtoms=4 and NumCells=4 Warning: probeset <hsa-mir-1226-star_st> has NumAtoms=4 and NumCells=4 Warning: probeset <hsa-mir-1228-star_st> has NumAtoms=4 and NumCells=4 Warning: probeset <hsa-mir-664-star_st> has NumAtoms=4 and NumCells=4 Warning: probeset <mdv1-mir-m9-star_st> has NumAtoms=4 and NumCells=4 Warning: probeset <cfa-mir-219-star_st> has NumAtoms=4 and NumCells=4 ?? <52900> records imported...Finished ?? PM/MM statistics: ????? 6703 cells with minimum number of PM/MM pairs: 2 ????? 78 cells with maximum number of PM/MM pairs: 47 New dataset <mirna-1_0> is added to Content... Importing </home> as <mirna-1_0.prb>... Note: The following header columns are missing: <serial order=""> ?? <46227> records read...Finished ?? <52900> records imported...Finished ?? probe info: ????? GC content: minimum GC is <0>? maximum GC is <25> ????? Melting Tm: minimum Tm is <35>? maximum Tm is <95> Importing </home> as <mirna-1_0.ann>... Error: wrong token number for <> Error when reading file </home>. Errore in import.expr.scheme("Scheme_miRNA_1_0", filedir = scmdir, paste(libdir,? : ? error in function ?ImportExprSchemes? I think that mirna_probe or annotation files from affymetrix aren't in the correct format or somewhat is missing probably. Thanks. Best regards. Giacomo down here my code: libdir <- "/home/user/exp/lib" scmdir <- "/home/user/exp/scheme" anndir <- "/home/user/exp/ann" scheme.mirna <- import.expr.scheme("Scheme_miRNA_1_0",filedir=scmdir, paste(libdir,"miRNA-1_0.CDF",sep="/"),paste(libdir,"miRNA- 1_0.probe.tab",sep="/"),annotfile=paste(anndir,"miRNA- 1_0.annot.csv",sep="/")) -- Dr. Giacomo Tuana Franguel Genopolis Consortium University of Milano-Bicocca Dept. of Biotechnology and Bioscience/ U4 Piazza della Scienza 4 20126 Milano, Italy Tel +39 02 6448 3530 Fax +39 02 6448 3550 http://www.genopolis.it Press ENTER to look up in Wiktionary or CTRL+ENTER to look up in Wikipedia

Dear Giacomo, Please use only the cdf and probe.tab files to create the scheme for miRNA. The reason is that the miRNA annotation does not follow the usual Affymetrix format for annotation files and thus can currently not be used to create the scheme file. You need to import the annotation file directly into R using read.csv(). 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 5/24/10 1:02 PM, giacomo.tuana at unimib.it wrote: > Dear list, > > > > I downloaded the three files (cdf, annotation, probes) from Affymetrix > website; but I got the following error from using xps and mirna > affymetrix annotation file. > > Warning: probeset <mml-mir-1224-star_st> has NumAtoms=4 and NumCells=4 > Warning: probeset <hsa-mir-1226-star_st> has NumAtoms=4 and NumCells=4 > Warning: probeset <hsa-mir-1228-star_st> has NumAtoms=4 and NumCells=4 > Warning: probeset <hsa-mir-664-star_st> has NumAtoms=4 and NumCells=4 > Warning: probeset <mdv1-mir-m9-star_st> has NumAtoms=4 and NumCells=4 > Warning: probeset <cfa-mir-219-star_st> has NumAtoms=4 and NumCells=4 > <52900> records imported...Finished > PM/MM statistics: > 6703 cells with minimum number of PM/MM pairs: 2 > 78 cells with maximum number of PM/MM pairs: 47 > New dataset <mirna-1_0> is added to Content... > Importing </home> as <mirna- 1_0.prb="">... > Note: The following header columns are missing: > <serial order=""> > <46227> records read...Finished > <52900> records imported...Finished > probe info: > GC content: minimum GC is <0> maximum GC is <25> > Melting Tm: minimum Tm is <35> maximum Tm is <95> > Importing </home> as <mirna- 1_0.ann="">... > Error: wrong token number for <> > Error when reading file </home>. > Errore in import.expr.scheme("Scheme_miRNA_1_0", filedir = scmdir, > paste(libdir, : > error in function ?ImportExprSchemes? > > I think that mirna_probe or annotation files from affymetrix aren't in > the correct format or somewhat is missing probably. > > > Thanks. > > > Best regards. > > Giacomo > > > down here my code: > > libdir <- "/home/user/exp/lib" > scmdir <- "/home/user/exp/scheme" > anndir <- "/home/user/exp/ann" > scheme.mirna <- import.expr.scheme("Scheme_miRNA_1_0",filedir=scmdir, > paste(libdir,"miRNA-1_0.CDF",sep="/"),paste(libdir,"miRNA- 1_0.probe.tab",sep="/"),annotfile=paste(anndir,"miRNA- 1_0.annot.csv",sep="/")) > > >

Dear Giacomo, Steve Shen was so kind to set up centralized scheme file repository at: http://microarray.bu.edu/~sshen/xps/ so you can download now the scheme "mirna10.root" from this repository. An official announcement of the availability will follow once the scheme list is complete. Best regards Christian On 5/24/10 1:02 PM, giacomo.tuana at unimib.it wrote: > Dear list, > > > > I downloaded the three files (cdf, annotation, probes) from Affymetrix > website; but I got the following error from using xps and mirna > affymetrix annotation file. > > Warning: probeset <mml-mir-1224-star_st> has NumAtoms=4 and NumCells=4 > Warning: probeset <hsa-mir-1226-star_st> has NumAtoms=4 and NumCells=4 > Warning: probeset <hsa-mir-1228-star_st> has NumAtoms=4 and NumCells=4 > Warning: probeset <hsa-mir-664-star_st> has NumAtoms=4 and NumCells=4 > Warning: probeset <mdv1-mir-m9-star_st> has NumAtoms=4 and NumCells=4 > Warning: probeset <cfa-mir-219-star_st> has NumAtoms=4 and NumCells=4 > <52900> records imported...Finished > PM/MM statistics: > 6703 cells with minimum number of PM/MM pairs: 2 > 78 cells with maximum number of PM/MM pairs: 47 > New dataset <mirna-1_0> is added to Content... > Importing </home> as <mirna- 1_0.prb="">... > Note: The following header columns are missing: > <serial order=""> > <46227> records read...Finished > <52900> records imported...Finished > probe info: > GC content: minimum GC is <0> maximum GC is <25> > Melting Tm: minimum Tm is <35> maximum Tm is <95> > Importing </home> as <mirna- 1_0.ann="">... > Error: wrong token number for <> > Error when reading file </home>. > Errore in import.expr.scheme("Scheme_miRNA_1_0", filedir = scmdir, > paste(libdir, : > error in function ?ImportExprSchemes? > > I think that mirna_probe or annotation files from affymetrix aren't in > the correct format or somewhat is missing probably. > > > Thanks. > > > Best regards. > > Giacomo > > > down here my code: > > libdir <- "/home/user/exp/lib" > scmdir <- "/home/user/exp/scheme" > anndir <- "/home/user/exp/ann" > scheme.mirna <- import.expr.scheme("Scheme_miRNA_1_0",filedir=scmdir, > paste(libdir,"miRNA-1_0.CDF",sep="/"),paste(libdir,"miRNA- 1_0.probe.tab",sep="/"),annotfile=paste(anndir,"miRNA- 1_0.annot.csv",sep="/")) > > >