[BioC] GEOquery - was queryGEO fails on GDS files (GEO Datasets)

Peter bioconductor-mailinglist at maubp.freeserve.co.uk
Wed Jan 11 21:21:16 CET 2006

Sean Davis wrote:
>I have recently uploaded a new package to bioconductor called GEOquery.

A follow up question, if I generate an expression set like so:

gds <- getGEO(filename='GDS1099.soft')
eset <- GDS2eSet(gds, do.log2=TRUE)

Then this works:

> sampleNames(eset)
  [1] "GSM37063" "GSM37064" "GSM37065" "GSM37066" "GSM37067"
  [6] "GSM37068" "GSM37069" "GSM37070" "GSM37071" "GSM37072"
[11] "GSM37073" "GSM37074" "GSM37075" "GSM37076" "GSM37077"

But this does not:

> geneNames(eset)

getGEO seems to parse the ID (and the IDENTIFIER) columns fine, so I'm
guessing that this is a problem in GDS2eSet.

I would expect to get "AFFX-BioB-5_at", "AFFX-BioC-3_at", ... back as
the geneNames values.

I'm using:

R Version 2.1.1  (2005-06-20)
Windows XP


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