Glazko, Galina <galina_glazko at="" ...=""> writes: > > Dear all, > > When I am trying to use GEOquery package, I get an error message: > > > gse <- getGEO("GSE1132") > > trying URL > 'ftp://ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE462_family.sof t.gz > ' > > Error in download.file(myurl, destfile, mode = mode) : > > cannot open URL > 'ftp://ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE462_family.sof t.gz > ' > > May be I have to update the package or reinstall? > > Thank you! > > Galina > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at ... > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > Hi Galina, There is a way to ovecome this problem. Follow these steps: 1. Open GEOquery directory under "C:\Program Files\R\R-2.2.1\library\GEOquery" 2. Open R. You should notice 'GEOquery' file. 3. Open it is a text editor (Notepad, Wordpad etc). Scroll the file to line#309. 4. You are in getGEOfile function. You should notice blocks of code that give specific instructions depending on the file type. At ln 309, change the ftp URL to: gseurl <- 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/' 5. Save the file...and you should be set. It worked for me. If you have problems again, probably you might want to restart R. But I must tell you that it takes a long time to load the GSE dataset...have patience. Thanks, Chaitanya

On Friday 29 September 2006 11:51, Chaitanya Acharya wrote: > Glazko, Galina <galina_glazko at="" ...=""> writes: > > Dear all, > > > > When I am trying to use GEOquery package, I get an error message: > > > gse <- getGEO("GSE1132") > > > > trying URL > > 'ftp://ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE462_family.s oft.gz > > ' > > > > Error in download.file(myurl, destfile, mode = mode) : > > > > cannot open URL > > 'ftp://ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE462_family.s oft.gz > > ' > > > > May be I have to update the package or reinstall? > > > > Thank you! > > > > Galina > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at ... > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > Hi Galina, > There is a way to ovecome this problem. > Follow these steps: > > 1. Open GEOquery directory under "C:\Program > Files\R\R-2.2.1\library\GEOquery" 2. Open R. You should notice 'GEOquery' > file. > 3. Open it is a text editor (Notepad, Wordpad etc). Scroll the file to > line#309. 4. You are in getGEOfile function. You should notice blocks of > code that give specific instructions depending on the file type. At ln 309, > change the ftp URL to: gseurl <- > 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/' 5. Save the > file...and you should be set. It worked for me. If you have problems again, > probably you might want to restart R. Hi, Chaitanya. Note that simply updating GEOquery will fix this problem. Sean