Dear Mayte Please read the following thread and my answers: https://www.stat.math.ethz.ch/pipermail/bioconductor/2009-February/026 358.html As I mentioned already, release 4 (r4) of the HuGene array converts it to an exon array, see: https://www.stat.math.ethz.ch/pipermail/bioconductor/2009-February/026 472.html This mail contains the code to use to create the scheme for HuGene and for doing rma analysis, i.e. you need to download also the probeset annotation file from Affymetrix and use function "import.exon.scheme()" to create the scheme. Alternatively, you could download the old release 3 (r3) files from Affymetrix and use "import.genome.scheme()". Best regards Christian Mayte Suarez-Farinas wrote: > Thanks to everybody that answer my previous post!!! > I succeed in working creating a root. scheme!!. > RMA run fine but the results have only 57 genes... > Here is my code. Any help will be appreciated. > > Thanks > > Mayte > > > library(xps) > ### define directories: > # directory containing Affymetrix library files > libdir <- "/Users/Mayte/Rlibrary/AffyDB/libraryfiles" > # directory containing Affymetrix annotation files > anndir <- "/Users/Mayte/Rlibrary/AffyDB/Annotation" > # directory to store ROOT scheme files > scmdir <- "/Users/Mayte/Rlibrary/AffyDB/ROOTSchemes" > > scheme.hugene10stv1r4.na28 <- 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="/")) > > scheme.hugene10stv1r4 <- root.scheme(paste(scmdir, > "Scheme_HuGene10stv1r4_na28.root",sep = "/")) > G1ST_data<-import.data(scheme.hugene10stv1r4, "Pamela_G1ST_dataxps", > celdir=getwd(), celfiles = thecelfiles, verbose = FALSE) > G1ST_rma_xps <- rma(G1ST_data, filename="Test3RMA",tmpdir="", > background="antigenomic",normalize=T,exonlevel="metacore+affx") > > str(G1ST_rma_xps at data) > data.frame': 57 obs. of 10 variables: > > > > On Apr 7, 2009, at 3:34 PM, cstrato wrote: > > >> Dear Mayte >> >> Martin was already so kind to answer your question where to find >> the Affymetrix files. >> >> In general you can select any array you want from: >> http://www.affymetrix.com/products_services/index.affx >> >> Thus, when selecting HuGene array you can download all necessary >> files from: >> http://www.affymetrix.com/products_services/arrays/specific/ >> hugene_1_0_st.affx#1_6 >> >> Furthermore, you can select the annotation files for e.g. na28 from: >> http://www.affymetrix.com/analysis/downloads/na28/ >> >> Please note that release 4 (r4) of the HuGene array converts it to >> an exon array, see: >> https://www.stat.math.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 >> _._._._._._._._._._._._._._._._._._ >> >> >> Mayte Suarez-Farinas wrote: >> >>> Hi, >>> I am trying to use xps to work with HuGene 1.0 >>> I have already ROOT and xps and I am following >>> their code to create the root scheme. The use of this packages are >>> more laborious that the annotation "ways' for other affychip, >>> but I am doing by best. For what I understand >>> I have to download HuGene-1_0-st-v1.r4.clf,HuGene-1_0-st- >>> v1.na28.hg18.transcript.csv >>> and HuGene-1_0-st-v1.r4.pgf form Affywebsite. I was able to find >>> the first two but not the >>> last one. ie: HuGene-1_0-st-v1.r4.pgf >>> >>> any help?? >>> >>> >>> scheme.hugene10stv1r3.na27 <- 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="/")) >>> >>> Mayte >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 >>> >>> >>> >>> > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > > >