[BioC] failure in GDS2eSet() in package GEOquery

[Sean Davis]

Wittner, Ben, Ph.D. wrote:
> Hello,
> 
> If I execute the following three lines:
> 
> library('GEOquery')
> gds <- getGEO('GSE2034')
> eset <- GDS2eSet(gds)

Hi, Ben.  NCBI GEO nomenclature can be tedious at times.  A GSE record
is not the same as a GDS record.  GDS2eSet() will only work on GDS
records, not GSE records.  I have made some relatively recent changes to
GEOquery to allow loading of GSEMatrix records from GEO.

> gseSetList <- getGEO('GSE2034',GSEMatrix=TRUE)


> names(gseSetList)
[1] "GSE2034_series_matrix-1.txt.gz" "GSE2034_series_matrix-2.txt.gz"

It turns out that the GSE is too big for MS Excel (NCBI GEO targeted
these files for Excel!), so two files are needed.  If you look at either
member of the gseSetList, you will see that each is an ExpressionSet
that you can simply combine.

Hope that helps.

Sean