[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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