An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20060713/ 5519674d/attachment.pl

You can't. The information in the GSE object and the exprSet object contain probeset summary data i.e the summary of 11 probes into 1 probeset value. rma uses all probes to create a probeset summary too. You need the CEL files and only some GEO entries supply these-- although occasionally the SOFT files contain rma data already. Stephen Henderson Wolfson Inst. for Biomedical Research Cruciform Bldg., Gower Street University College London United Kingdom, WC1E 6BT +44 (0)207 679 6827 -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Alberto Goldoni Sent: 13 July 2006 11:19 To: bioconductor at stat.math.ethz.ch Subject: [BioC] problem to obtain exprset using GEOquery I have converted a GSE object to an exprSet object "eset2" just in the vignette but I wanna analyze microarray dataset again for example with: usually starting from CEL files i should edit: data<-ReadAffy(widget=T) pData(data) and then: data.rma<-rma(data) # for example! BUT STARTING FROM THE exprSet object "eset2" HOW CAN PROCEDE IN ORDER TO reanalyze microarray if i write: eset2.rma<-rma(eset2) Errore in probeNames(object, subset) : no direct or inherited method for function 'probeNames' for this call where > eset2 Expression Set (exprSet) with 22283 genes 76 samples phenoData object with 1 variables and 76 cases varLabels : samples how can I do to create an affybatch object in order to use rma function on my dataset? ps: to obtain eset2 I have followed the instruction on the GEOquery vignette: > probesets <- Table(GPLList(gse)[[1]])$ID > data.matrix <- log2(do.call("cbind", lapply(GSMList(gse), function(x) { + tab <- Table(x) + mymatch <- match(probesets, tab$ID_REF) + return(tab$VALUE[mymatch]) + }))) > rownames(data.matrix) <- probesets > colnames(data.matrix) <- names(GSMList(gse)) > pdata <- data.frame(samples = names(GSMList(gse))) > rownames(pdata) <- names(GSMList(gse)) > pheno <- new("phenoData", pData = pdata, varLabels = as.list("samples")) > eset2 <- new("exprSet", exprs = data.matrix, phenoData = pheno) > eset2 Dr Alberto Goldoni Medical Genetics Unit S. Orsola-Malpighi Hospital Via Massarenti n.9, Pad 11 40100 Bologna, Italy Mobile Phone: 338-4145970 Fax: 051-636-4004 <mailto:alberto.goldoni at="" eurogene.org=""> alberto.goldoni at eurogene.org <http: www.eurogene.org=""> www.eurogene.org <http: www.lagem.it=""> www.lagem.it [[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 ********************************************************************** This email and any files transmitted with it are confidentia...{{dropped}}