Here is what I am doing:
#GDS download and processing test source("http://bioconductor.org/biocLite.R") biocLite() library(GEOquery) gds <- getGEO('GDS756') #Convert to ExpressionSet eset <- GDS2eSet(gds,do.log2=TRUE)
eset is summarized like this:
ExpressionSet (storageMode: lockedEnvironment) assayData: 22283 features, 6 samples element names: exprs protocolData: none phenoData sampleNames: GSM21712 GSM21713 ... GSM21718 (6 total) varLabels: sample disease.state description varMetadata: labelDescription featureData featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (22283 total) fvarLabels: ID Gene title ... GO:Component ID (21 total) fvarMetadata: Column labelDescription experimentData: use 'experimentData(object)' pubMedIds: 16531451 Annotation:
What I want is to output a table in a text file, containing the following columns: (Affymetrix probe ID, ENTREZ Gene ID, expression for sample 1, ..., expression for sample n).
Weirdly enough, GEOQuery manual says that eset should not contain annotated genes, but it seems from my basic object inspection that the featureData contains just that. However my R knowledge is limited so I was unable to produce my table from it.