[BioC] specifying filenames and celfile.path to ReadAffy()

Gordon Smyth smyth at wehi.edu.au
Fri Aug 27 09:26:44 CEST 2004


Am I right in thinking that arguments filenames and celfile.path cannot 
both be specified to ReadAffy()? So one can't use celfile.path to specify 
certain CEL files to be read from a specified directory?

This is fine:

 > dir(celpath)
[1] "binary.cel" "text.cel"
 > abatch <- ReadAffy(celfile.path=celpath)

but any attempt to specify filenames at the same time fails:

 >   abatch <- ReadAffy("text.cel",celfile.path=celpath)
Error in read.affybatch(filenames = filenames, phenoData = phenoData,  :
         Could not open file text.cel
 >   abatch <- ReadAffy(filenames="text.cel",celfile.path=celpath)
Error in read.affybatch(filenames = filenames, phenoData = phenoData,  :
         Could not open file text.cel

So to read specified files from a specified directory, one should give a 
vector of full path names:

abatch <- ReadAffy(filenames=file.path(celpath,"text.cel"))

Is this the recommended way to do it?

Gordon



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