I have some problem with importing data using GEOquery. I download an ExpressionSet for some further analysis, however in my record only few GSMs from all are interesting for me. My question is how to modify my code to download only the selected GSMs and analyze it further with limma package. I am grateful for any suggestions.
eset<-getGEO('GSE13937')[] -----> but I would like the data only for e.g. GSM26056, GSM26076, GSM26102, and GSM26123
And, then perform a standard analysis like:
design <-cbind(normal=c(1,1,0,0), tumour=c(0,0,1,1)) c <-makeContrasts(normal-tumour,levels=design) fit <-lmFit(eset, design) fit2 <-contrasts.fit(fit,c) fit2 <-eBayes(fit2) glist <-topTable(fit2, n=50, adjust="BH", sort.by="P", p.value=0.01)