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Hi Dennis, Wall, Dennis Paul wrote: > I am trying to download the file gds1917 from GEO using getGEO, but am > receiving an error > > >>library(GEOquery) > > >>gds <- getGEO("gds1917") > > > trying URL > 'ftp://ftp.ncbi.nih.gov/pub/geo/data/gds/soft_gz/GDS1917.soft.gz' > > Error in download.file(myurl, destfile, mode = mode) : > > cannot open URL > 'ftp://ftp.ncbi.nih.gov/pub/geo/data/gds/soft_gz/GDS1917.soft.gz' > > > > it looks like getGEO is looking in the wrong place for the file. The ftp > address is actually > > ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS1917.soft.gz > > > > am I doing something wrong? You didn't give us your sessionInfo(), so I have to fly blind here, but I assume you are using an old version of R, and hence an old version of GEOquery. URLs are notoriously unstable, so for any package that queries a webserver there are often updates that contain the new URL. > library(GEOquery) > gds <- getGEO("gds1917") trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS1917.soft.gz' ftp data connection made, file length 5267985 bytes opened URL downloaded 5144Kb File stored at: C:\WINDOWS\TEMP\Rtmpy3lkrb/GDS1917.soft.gz parsing geodata parsing subsets ready to return > sessionInfo() R version 2.4.1 (2006-12-18) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" other attached packages: GEOquery "1.8.0" Best, Jim > > > > Thank you, > > > > Dennis > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

On Thursday 25 January 2007 14:29, Wall, Dennis Paul wrote: > I am trying to download the file gds1917 from GEO using getGEO, but am > receiving an error > > > library(GEOquery) > > > > gds <- getGEO("gds1917") > > trying URL > 'ftp://ftp.ncbi.nih.gov/pub/geo/data/gds/soft_gz/GDS1917.soft.gz' > > Error in download.file(myurl, destfile, mode = mode) : > > cannot open URL > 'ftp://ftp.ncbi.nih.gov/pub/geo/data/gds/soft_gz/GDS1917.soft.gz' > > > > it looks like getGEO is looking in the wrong place for the file. The ftp > address is actually > > ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS1917.soft.gz > > > > am I doing something wrong? Just an update of GEOquery will do the trick. Sean