Hi!

While trying to get data from GEO for "GSE47204", I get an expressionSet as first element of the list. My R environment tells that the size of the expressionSet is 475.2 Mb, but the object lacks any feature data. Are the data stored in some other place/slot, and then how to access it?

Appreciate any help.

Zeeshan

> show(gse1)
ExpressionSet (storageMode: lockedEnvironment)
assayData: 0 features, 30 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM1146803 GSM1146804 ... GSM1146832 (30
    total)
  varLabels: title geo_accession ... data_row_count (41
    total)
  varMetadata: labelDescription
featureData
  featureNames:
  fvarLabels: ID dbSNP RS ID ... RANGE_END (9 total)
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
Annotation: GPL16131 

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_India.1252 
[2] LC_CTYPE=English_India.1252   
[3] LC_MONETARY=English_India.1252
[4] LC_NUMERIC=C                  
[5] LC_TIME=English_India.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets 
[7] methods   base     

other attached packages:
[1] BiocInstaller_1.20.1 GEOquery_2.36.0     
[3] Biobase_2.30.0       BiocGenerics_0.16.1 

loaded via a namespace (and not attached):
[1] tools_3.2.2    RCurl_1.95-4.7 bitops_1.0-6   XML_3.98-1.3 

You are getting an empty data set because that's what the submitters submitted. The only thing you download of any size is the GPL that describes the array, so I think that's the bulk of your download.

I'm not familiar with this array, but it seems to be some sort of a SNP chip. You can always download the celfiles and use ChAS to analyze the data, as I don't think there is a way in bioconductor to do any analysis of the raw data.
 

Thanks James for the support, it will avoid a lot of unnecessary struggling.

Z