Hi I have downloaded a GSE file (GSE21111_family.soft.gz). And using the GEOquery package documentation creating the expression set from the GSE file. Here is that script. library(GEOquery) u <- getGEO(filename=GSE21111_family.soft.gz,GSEMatrix=TRUE) probesets <- Table(GPLList(u)[[1]])$ID data.matrix <- do.call("cbind",lapply(GSMList(u), function(x) { tab <- Table(x) mymatch <- match(probesets, tab$ID_REF) return(tab$VALUE[mymatch])})) data.matrix <- apply(data.matrix,2,function(x) { as.numeric(as.character(x)) }) rownames(data.matrix)<- probesets colnames(data.matrix) <- names(GSMList(u)) pdata <- data.frame(samples=names(GSMList(u))) rownames(pdata) <- names(GSMList(u)) pheno <- as(pdata, "AnnotatedDataFrame") eset <- new("ExpressionSet",exprs=data.matrix,phenoData=pheno) pData(eset) samplenames.................. Now when i did pData(eset), it gives me the sampleNames only. But along with samplenames i also want sample conditions like controll and clinical isolates). Kindly tell me how i include these information. i am also wondering about one thing when we use download GSE2111 file directly from internet using u <- getGEO(GSE21111) , then u is an expression set and get the full phenodata information. Regards~ Reema Singh [[alternative HTML version deleted]]

Hi, Reema. The recommended way of getting a GSE into an ExpressionSet is to use a GSE Matrix file. eset = getGEO('GSE21111')[[1]] If you want to store the downloaded file in a convenient place for the future, specify a download directory in the getGEO call. Hope that helps. Sean On Sat, Nov 5, 2011 at 6:33 AM, Reema Singh <reema28sep at="" gmail.com=""> wrote: > Hi > > I have downloaded a GSE file (GSE21111_family.soft.gz). And using the > GEOquery package documentation creating the expression set from the GSE > file. Here is that script. > > library(GEOquery) > u <- getGEO(filename=GSE21111_family.soft.gz,GSEMatrix=TRUE) > ?probesets <- Table(GPLList(u)[[1]])$ID > ? ? ? ?data.matrix <- do.call("cbind",lapply(GSMList(u), function(x) { > ? ? ? ?tab <- Table(x) > ? ? ? ?mymatch <- match(probesets, tab$ID_REF) > ? ? ? ?return(tab$VALUE[mymatch])})) > ? ? ? ?data.matrix <- apply(data.matrix,2,function(x) { > ? ? ? ?as.numeric(as.character(x)) }) > ? ? ? ?rownames(data.matrix)<- probesets > ? ? ? ?colnames(data.matrix) <- names(GSMList(u)) > ? ? ? ?pdata <- data.frame(samples=names(GSMList(u))) > ? ? ? ?rownames(pdata) <- names(GSMList(u)) > ? ? ? ?pheno <- as(pdata, "AnnotatedDataFrame") > ? ? ? ?eset <- new("ExpressionSet",exprs=data.matrix,phenoData=pheno) > ? ? ? ?pData(eset) > ? ? ? ? samplenames.................. > > > Now when i did pData(eset), it gives me the sampleNames only. But along > with samplenames i also want sample conditions like controll and clinical > isolates). Kindly tell me how i include these information. > i am also wondering about one thing when we use download GSE2111 file > directly from internet using u <- getGEO(GSE21111) , then u is an > expression set and get the full phenodata information. > > Regards~ > Reema Singh > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >