Dear list, Recently I tried to use xps package to process Affymetrix Human Gene 1.0 ST Array data. It seems that all low level analysis is fine. But there are always problems with rma function from my many tires, specifically, rma always gives me expression data of 57 genes (?). Also I don't see Affy probeset names in the rma output. Please see my codes below: > scheme <- import.genome.scheme("Scheme_HuGene10stv1r4_na28",filedir=scmdir, paste(libdir,"HuGene-1_0-st-v1.r4.clf",sep="/"), paste(libdir,"HuGene-1_0-st-v1.r4.pgf",sep="/"), paste(anndir,"HuGene-1_0-st-v1.na28.hg18.transcript.csv",sep="/")) Creating new file </applications>... Importing </applications> as <hugene-1_0-st-v1.cxy>... <1102500> records imported...Finished New dataset <hugene-1_0-st-v1> is added to Content... Importing </applications> as <hugene-1_0-st-v1.ann>... Number of transcripts is <33297>. <861493> records imported...Finished <257430> total transcript units imported. Genome cell statistics: Number of unit cells: minimum = 1, maximum = 1189 Finishedsetwd('/Users/zhujack/Documents/Work/Projects/dan/Affy') > data <- import.data( scheme, "Dan_affy", celdir = celdir, celfiles = celfiles) Opening file </applications> in <read> mode... Creating new file </users>... Importing <./CMPC_WT_Test_run.CEL> as <cmpc_wt_test_run.cel>... <1102500> records imported... hybridization statistics: 2 cells with minimal intensity 32 2 cells with maximal intensity 65534 New dataset <dataset> is added to Content... Importing <./CMPC_WT_Test_run2.CEL> as <cmpc_wt_test_run2.cel>... <40001> records imported... > data.rma <- rma(data,"Dan_Affy_RMA", ,tmpdir="", background="antigenomic", normalize=T, exonlevel="metacore+affx") Creating new file </users>... Opening file </applications> in <read> mode... Opening file </users> in <read> mode... Preprocessing data using method <preprocess>... Background correcting raw data... setting selector mask for typepm <8252> calculating background for <cmpc_wt_test_run.cel>... background statistics: 1097995 cells with minimal intensity 0 6 cells with maximal intensity 60.8093 calculating background for <cmpc_wt_test_run2.cel>... calculating expression for <57> of <257430> units...Finished. expression statistics: minimal expression level is <3.52152> maximal expression level is <6634.65> preprocessing finished. Opening file </applications> in <read> mode... Opening file </users> in <read> mode... Opening file </users> in <read> mode... Exporting data from tree <*> to file </users>... Reading entries from <hugene-1_0-st-v1.ann> ...Finished <57> of <57> records exported. ---------- Your help will be greatly appreciated. Jack -- Yuelin Jack Zhu Genetics Branch/CCR/NCI/NIH Tel: (301)496-4527 FAX: (301) 402-3241 E-mail: zhujack at mail.nih.gov

Dear Jack, Please note that with release r4 Affymetrix has converted HuGene to an exon array, thus you need either to use the old r3 CLF/PGF files or use "import.exon.scheme". For more details please see: https://stat.ethz.ch/pipermail/bioconductor/2009-February/026360.html https://stat.ethz.ch/pipermail/bioconductor/2009-February/026472.html 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 _._._._._._._._._._._._._._._._._._ Zhu, Jack (NIH/NCI) [C] wrote: > Dear list, > > Recently I tried to use xps package to process Affymetrix Human Gene 1.0 ST > Array data. It seems that all low level analysis is fine. But there are > always problems with rma function from my many tires, specifically, rma > always gives me expression data of 57 genes (?). Also I don't see Affy > probeset names in the rma output. > > Please see my codes below: > > >> scheme <- import.genome.scheme("Scheme_HuGene10stv1r4_na28",filedir=scmdir, >> > paste(libdir,"HuGene-1_0-st-v1.r4.clf",sep="/"), > paste(libdir,"HuGene-1_0-st-v1.r4.pgf",sep="/"), > paste(anndir,"HuGene-1_0-st-v1.na28.hg18.transcript.csv",sep="/")) > > Creating new file > </applications>... > Importing </applications> as > <hugene-1_0-st-v1.cxy>... > <1102500> records imported...Finished > New dataset <hugene-1_0-st-v1> is added to Content... > Importing > </applications> as > <hugene-1_0-st-v1.ann>... > Number of transcripts is <33297>. > <861493> records imported...Finished > <257430> total transcript units imported. > Genome cell statistics: > Number of unit cells: minimum = 1, maximum = 1189 > Finishedsetwd('/Users/zhujack/Documents/Work/Projects/dan/Affy') > > > >> data <- import.data( scheme, "Dan_affy", celdir = celdir, celfiles = celfiles) >> > > Opening file </applications> in > <read> mode... > Creating new file > </users>... > Importing <./CMPC_WT_Test_run.CEL> as <cmpc_wt_test_run.cel>... > <1102500> records imported... > hybridization statistics: > 2 cells with minimal intensity 32 > 2 cells with maximal intensity 65534 > New dataset <dataset> is added to Content... > Importing <./CMPC_WT_Test_run2.CEL> as <cmpc_wt_test_run2.cel>... > <40001> records imported... > > >> data.rma <- rma(data,"Dan_Affy_RMA", ,tmpdir="", background="antigenomic", >> > normalize=T, exonlevel="metacore+affx") > > Creating new file > </users>... > Opening file </applications> in > <read> mode... > Opening file > </users> in > <read> mode... > Preprocessing data using method <preprocess>... > Background correcting raw data... > setting selector mask for typepm <8252> > calculating background for <cmpc_wt_test_run.cel>... > background statistics: > 1097995 cells with minimal intensity 0 > 6 cells with maximal intensity 60.8093 > calculating background for <cmpc_wt_test_run2.cel>... > calculating expression for <57> of <257430> units...Finished. > expression statistics: > minimal expression level is <3.52152> > maximal expression level is <6634.65> > preprocessing finished. > Opening file </applications> in > <read> mode... > Opening file > </users> in > <read> mode... > Opening file > </users> in > <read> mode... > Exporting data from tree <*> to file > </users>... > Reading entries from <hugene-1_0-st-v1.ann> ...Finished > <57> of <57> records exported. > > ---------- > Your help will be greatly appreciated. > > Jack > -- > Yuelin Jack Zhu > > Genetics Branch/CCR/NCI/NIH > Tel: (301)496-4527 > FAX: (301) 402-3241 > E-mail: zhujack at mail.nih.gov > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >