[BioC] GEOquery Data structure: GSEMatrix

[Hendrik Falk]

Hi list,

I'm trying to download GSE11595. It throws an error (see below) when I try to
download as GSEMatrix=TRUE, but runs through with tons of warnings under the
GSEMatrix=FALSE parameter. R is up-to-date, a clean install (sessionInfo below).

Is there a way to fix the download as GSEMatrix=TRUE, as I prefer the resulting data
structure?

Many thanks,
Hendrik


> GSE11595<-getGEO("GSE11595",GSEMatrix=TRUE)
Found 2 file(s)
GSE11595-GPL3906_series_matrix.txt.gz
trying URL
'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE11595/GSE11595-GPL3906_series_matrix.txt.gz'
ftp data connection made, file length 59641 bytes
opened URL
downloaded 58 Kb

Error in `rownames<-`(`*tmp*`, value = c(2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L,  :
  attempt to set rownames on object with no dimensions



> sessionInfo()
R version 2.14.2 (2012-02-29)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252   
LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                      
LC_TIME=English_Australia.1252

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

other attached packages:
[1] GEOquery_2.21.9 Biobase_2.14.0

loaded via a namespace (and not attached):
[1] RCurl_1.91-1.1 XML_3.9-4.1




-- 
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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