Hello,

I tried to use GEOQuery package of BioC. It does not download GSE. 
I investigated problem, understood that the problem was about internal function "download".
Reccomendations about it mostly suggest switching any proxy off in R. I did, and nothing changed.

> getGEO(GEO="GSE1")
Found 1 file(s)
GSE1_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE1/GSE1_series_matrix.txt.gz'
Error in download.file(sprintf("ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/%s/%s", : 
 cannot open URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE1/GSE1_series_matrix.txt.gz'


I use Ubuntu Lucid 64 bit

Thanks

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