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/Se riesMatrix/%s/%s", : cannot open URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE 1/GSE1_series_matrix.txt.gz' I use Ubuntu Lucid 64 bit Thanks [[alternative HTML version deleted]]

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_ma trix.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_ma trix.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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]