[BioC] getGEO error?

[Hendrik Falk]

Hi list,

I'm trying to analyse GeneExpressionOmnibus data using the Biobase package. For the
GSE record GSE4922 I get an error as shown below, whereas other records (e.g.
GSE1456) load without problems. Is there an easy way to fix the problem or get
around it?

Best Regards,
Hendrik

> GSE4922 <- getGEO("GSE4922",GSEMatrix=TRUE)
Found 4 file(s)
GSE4922-GPL96_series_matrix-1.txt.gz
trying URL
'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE4922/GSE4922-GPL96_series_matrix-1.txt.gz'
ftp data connection made, file length 44890082 bytes
opened URL
downloaded 42.8 Mb

Using locally cached version of GPL96 found here:
C:\DOCUME~1\falk\LOCALS~1\Temp\RtmpAjqjX7/GPL96.soft
Error in validObject(.Object) :
  invalid class “ExpressionSet” object: featureNames differ between assayData and
featureData
>


-- 
Dr. Hendrik Falk
Senior Research Officer
High Throughput Chemical Screening Facility
The Walter and Eliza Hall Institute of Medical Research
Biotechnology Centre
4 Research Avenue
Bundoora Victoria
3086 Australia

Tel. (+61 3) 9345 2104
Fax.            - 2211
Mob. 0420 353572





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