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