Problems opening cel files
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@ranjita_duttaroy-9780
Last seen 5.4 years ago

 

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 • 1.4k views
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@james-w-macdonald-5106
Last seen 9 hours ago
United States

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.
 

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@ranjita_duttaroy-9780
Last seen 5.4 years ago

Thank you for your reply!

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