Question: getGEO GSEMatrix = TRUE error
1
gravatar for Lin
5.2 years ago by
Lin30
United States
Lin30 wrote:

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 urlĀ 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 usingĀ options('download.file.method'='curl') but it doesn't work for me.

Any ideas? Thank you in advance.

Lin

geoquery gsematrix • 2.7k views
ADD COMMENTlink modified 5.2 years ago by Sean Davis26k • written 5.2 years ago by Lin30
0
gravatar for Sean Davis
5.2 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

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.

ADD COMMENTlink modified 14 months ago by _r_am32k • written 5.2 years ago by Sean Davis26k

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.

ADD REPLYlink written 4.2 years ago by Lin30
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