Reading soft file data to R from a downloaded file

Question

[hasani.iut6]

I've been download soft file data from GSE47875 assertion number to my labtop. Now I want to load it to R, i've been used the

getGEO("GSE47875",filename = "Desktop/GSE47875/GSE47875_series_matrix.txt.gz")

command but I faced the following error:

sh: 1: curl: not found
File stored at: 
/tmp/RtmpHyQAgg/GPL1355.soft
Error in file(fname, "r") : cannot open the connection
In addition: Warning messages:
1: In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) :
  download had nonzero exit status
2: In file(fname, "r") :
  cannot open file '/tmp/RtmpHyQAgg/GPL1355.soft': No such file or directory

Where is the problem? how can load the soft file data to R?

Thank you,

mansoor

Answer 1

[hasani.iut6]

The problem was because that I've not been installed curl on my Linux, so I've installed it by the sudo apt-get install curl command and the problem was solved.

Answer 2

[h.mon]

From getGEO manual:

Either one of GEO or filename may be specified, not both

Answer 3

[hasani.iut6]

I've tested it to by this command:

data=getGEO(filename = "GSE47875/GSE47875_series_matrix.txt.gz")

but the error is still exsit:

sh: 1: curl: not found
File stored at: 
/tmp/Rtmp6zTEO1/GPL1355.soft
Error in file(fname, "r") : cannot open the connection
In addition: Warning messages:
1: In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) :
  download had nonzero exit status
2: In file(fname, "r") :
  cannot open file '/tmp/Rtmp6zTEO1/GPL1355.soft': No such file or directory