On Mon, May 3, 2010 at 2:55 PM, Sean Davis <seandavi at="" gmail.com=""> wrote: > On Sat, May 1, 2010 at 8:56 AM, Rahul Sharma <rahularjun86 at="" gmail.com=""> wrote: >> Hello Sir/Madam >> >> I am Rahul Sharma, Research fellow from New Delhi India, i need to do some >> analysis on the GDS1825 dataset, i am using the GEOquery package of >> Bioconductor, following error occurs when i try to fetch the >> link.....internet connection is there on my system dnt know why it is not >> connecting to the ftp.. >> >> ====================================================================== >> >>> library(GEOquery) >> Loading required package: Biobase >> >> Welcome to Bioconductor >> >> ?Vignettes contain introductory material. To view, type >> ?'openVignette()'. To cite Bioconductor, see >> ?'citation("Biobase")' and for packages 'citation(pkgname)'. >> >> Loading required package: RCurl >> Loading required package: bitops >>> gpl <- getGEO('GDS1825',destdir=".") >> Error in download.file(myurl, destfile, mode = mode, quiet = TRUE) : >> ?cannot open URL ' >> ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS1825.soft.gz' > > Hi, Rahul. > > This has nothing to do with GEOquery. ?The ftp site is broken at NCBI > GEO; I'm checking with them about the details. It appears they were rebuilding the ftp site, as the files are slowly being repopulated. The above code works here, at least. Sean