Entering edit mode
4.5 years ago
mahal1366
•
0
I am new in R. I am using 3.6.1 version of R on 64-bit system with Windows 7. In RStudio, when I attempt to run the getGEO command,
> library(Biobase)
> library(GEOquery)
> library(limma)
> gset <- getGEO("GSE41313", GSEMatrix =TRUE, AnnotGPL=TRUE)
I get the following error message
Found 1 file(s)
GSE41313_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE41nnn/GSE41313/matrix/GSE41313_series_matrix.txt.gz'
Error in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", :
cannot open URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE41nnn/GSE41313/matrix/GSE41313_series_matrix.txt.gz'
In addition: Warning message:
In download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", :
InternetOpenUrl failed: 'A connection with the server could not be established'
>
Have you been able to download data this way before? It is possible that your local firewall may be preventing this download since direct URL to download data is working.
I'm downloading this data for the first time . my windows firewall and antivirus is off.
I have no problem downloading packages. So I don't think it's an internet connection problem.
Are you able to use the URL I linked in the comment above (click on the bold link) and does that prompt you to save the file? If you have a firewall protecting your institution/site it may be preventing the download.
yes. I can download by this URL.
I think that there is something specific at your side that is causing the error. I can download the data:
There are parsing warnings, but these are noted in the GEO record (I believe), with code provided to correct them. If you go HERE, then click on the
Analyze with GEO2R
blue button, and then theR script
tab, you will see code to use.Thanks for your answers, I try to solve the problem.