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

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