Hello All,
I have been downloading GSE sets from GEO. This time I tried to download RNAseq data packaged as GSE. Unfortunately, the code I have been using produced empty file.
Would you please advise how to adjust my code for this dataset?
Thank you for your help.
Anita
gset <- getGEO("GSE67835", GSEMatrix =TRUE) if (length(gset) > 1) idx <- grep("GPL18573", attr(gset, "names")) else idx <- 1 gset67835 <- gset[[idx]]
gset67835
ExpressionSet (storageMode: lockedEnvironment)
assayData: 0 features, 328 samples
element names: exprs
protocolData: none
phenoData
sampleNames: GSM1657871 GSM1657872 ... GSM1658366 (328 total)
varLabels: title geo_accession ... supplementary_file_2 (44 total)
varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: GPL18573
Thank you for your reply.
Anita
Thank you for the hint. Would you please explain me more how to do the process? Actually I'm very new in this BIOdata field and I dont know exactly what to do. For my data (GSE81540), I dont have "_Raw.tar" part in the GEO website: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81540
So I'm wondering what should I do?
Appreciate your help.