getGEO GSEMatrix = TRUE error

Question

[Lin]

Dear Bioconductor users,

I am having problems using GEOquery. It won't download GEO dataset and I am getting the following error:

getGEO("GSE44281", GSEMatrix = TRUE);

ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE44nnn/GSE44281/matrix/

Found 1 file(s)
GSE44281_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE44nnn/GSE44281/matrix/GSE44281_series_matrix.txt.gz'
Error in download.file(sprintf("ftp://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s",  : 
  cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE44nnn/GSE44281/matrix/GSE44281_series_matrix.txt.gz'
In addition: Warning message:
In download.file(sprintf("ftp://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s",  :
  InternetOpenUrl failed: 'The FTP session was terminated

I know it's because of the ftp session because if I get the GSM file which uses http address it works.

I also know that if I go directly to this url ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE44nnn/GSE44281/matrix/GSE44281_series_matrix.txt.gz using browser, I can download the file and if I used wireless, I can download using R.

Someone in the other thread suggested using options('download.file.method'='curl') but it doesn't work for me.

Any ideas? Thank you in advance.

Lin

Answer 1

[Sean Davis]

You are likely behind a firewall, so you will likely need to define a proxy within R. See the help file for download.file(). You may need to work with your IT support group if you don't know what proxy to use.

[Lin]

Hopefully this reply helps someone. Turned out the problem was the combination of getGEO and R. It was encoded in such a way that this particular FTP download was blocked even though proxy was already setup correctly. I didn't find a solution other than using wireless connection to download this.