Question: Problems opening cel files
0
gravatar for ranjita_duttaroy
3.7 years ago by
ranjita_duttaroy0 wrote:

 

I have very basic knowledge in R, and I am following a workflow to do gene expression analysis of an already existing data set from GEO. The following commands are used for unzipping the cels.

untar("GSE27447_RAW.tar", exdir="data")
cels = list.files("data/", pattern = "CEL")
sapply(paste("data", cels, sep="/"), gunzip)

ERROR
cels = list.files("data/", pattern = "CEL")

I am using the commands above to unzip the files, but I am getting the following error message after sapply. Could somebody please tell me what this means? 

Error in FUN(X[[i]], ...) :
  Argument 'filename' and 'destname' are identical: data/
 

 

 

cel • 1.2k views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by ranjita_duttaroy0
Answer: Problems opening cel files
0
gravatar for James W. MacDonald
3.7 years ago by
United States
James W. MacDonald51k wrote:

You need to paste the complete output from running your command, not just selective portions. It's not clear from what you paste where the error occurred.

That said, it looks like it comes from the call to gunzip, in which case the error is saying that the files are already decompressed. In addition, do note that both the oligo and affy packages are quite happy to use gz compressed files, so it's not necessary to decompress anyway.
 

ADD COMMENTlink written 3.7 years ago by James W. MacDonald51k
Answer: Problems opening cel files
0
gravatar for ranjita_duttaroy
3.7 years ago by
ranjita_duttaroy0 wrote:

Thank you for your reply!

ADD COMMENTlink written 3.7 years ago by ranjita_duttaroy0
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