Hi All, I want to download the GSE or SOFT file in Bioconductor using GEOquery but its not working. Can any one suggest how can use GEOquery or other module in Bioconductor for GSE and SOFT file. Thanking you. -- Nitish Kumar Mishra 3104E, CBCB, Biomolecular Sciences Bldg #296 University of Maryland, College Park, MD 20742 Phone (Off): 301-405-8218 Mobile No: 240-898-7311 nitish@umiacs.umd.edu mishran@umd.edu [[alternative HTML version deleted]]

On Thu, Jun 9, 2011 at 10:25 AM, Nitish Kumar Mishra <nitishimtech at="" gmail.com=""> wrote: > Hi All, > I want to download the GSE or SOFT file in Bioconductor using GEOquery but > its not working. Can any one suggest how can use GEOquery or other module in > Bioconductor for GSE and SOFT file. Hi, Nitish. library(GEOquery) esetlist = getGEO('GSE2553') If that does not work for your GSE, could you post the commands that you are using, the error messages you receive, and the output of sessionInfo()? Thanks, Sean

Hi Nitish, I have come across this problem a few times on different systems. I think it's a problem with cURL, which GEOquery uses to download the GSEmatrix. After loading GEOquery try to update or install any package and you should see that it fails to download. This is because GEOquery changes the default download option in R to cURL. To change it back to 'auto' execute the command below and all should be well. options(download.file.method="auto") Do let me know how you get on. Regards, Fabio Liberante Analyse Genomics On 9 June 2011 15:25, Nitish Kumar Mishra <nitishimtech at="" gmail.com=""> wrote: > Hi All, > I want to download the GSE or SOFT file in Bioconductor using GEOquery but > its not working. Can any one suggest how can use GEOquery or other module in > Bioconductor for GSE and SOFT file. > > Thanking you. > > -- > Nitish Kumar Mishra > 3104E, CBCB, Biomolecular Sciences Bldg #296 > University of Maryland, College Park, MD 20742 > Phone (Off): 301-405-8218 > Mobile No: 240-898-7311 > nitish at umiacs.umd.edu > mishran at umd.edu > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >