On Wed, Dec 1, 2010 at 6:19 AM, Koray Kaya <koray@gmx.co.uk> wrote:

> 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.
>
>
Do you need to use a proxy to connect to the internet outside of R?  If so,
you may need to set the proxy in R, also.


> > 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
> '
>
>
Some people have reported that setting

options("download.file.method"="wget")

helps in this situation.  You could also try "curl" or "lynx".

If you still have problems, could you send the output of sessionInfo()?

Thanks,
Sean



>
> I use Ubuntu Lucid 64 bit
>
> Thanks
>
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