Question: Regarding GEOquery
0
gravatar for Nitish Kumar Mishra
8.5 years ago by
United States
Nitish Kumar Mishra30 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@umiacs.umd.edu mishran@umd.edu [[alternative HTML version deleted]]
geoquery • 443 views
ADD COMMENTlink modified 8.5 years ago by Fabio Liberante20 • written 8.5 years ago by Nitish Kumar Mishra30
Answer: Regarding GEOquery
0
gravatar for Sean Davis
8.5 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
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
ADD COMMENTlink written 8.5 years ago by Sean Davis21k
Answer: Regarding GEOquery
0
gravatar for Fabio Liberante
8.5 years ago by
Fabio Liberante20 wrote:
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 >
ADD COMMENTlink written 8.5 years ago by Fabio Liberante20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 217 users visited in the last hour