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 

Unfortunately, it appears that the submitters did not submit the data into GEO.  Instead, the data were actually submitted as .txt files, one per sample.  This means that it will be extra work for you to load this dataset and the approach for doing so is not something that is easily standardized.  GEOquery can help you get started:

getGEOSuppFiles('GSE67835')

This will download GSE67835_Raw.tar which you can untar, resulting in one file per sample.  You can then read these files into R one-at-a-time and attach the data to the existing ExpressionSet.