I have solved this issue with expresso. The problem was that I am a/an <insert preferred="" derogatory="" euphemism="" here=""> and masked the "normalize" function with the little macro function I wrote to perform these normalizations. Apologies, Eric -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Kort, Eric Sent: Monday, November 14, 2005 3:41 PM To: bioconductor at stat.math.ethz.ch Subject: [BioC] expresso still dying on list.files() I am still getting an error when trying to normalize an affybatch using expresso. I am running 64 bit R 2.2.0 (having upgraded per an earlier recommendation) on Suse 9.1. Here is my call, error, and traceback (and why is expresso calling AffyBatch again?) > AB <- ReadAffy(celfile.path="./") > eset <- expresso(AB, bgcorrect.method="mas", normalize.method="constant", pmcorrect.method="mas", summary.method="mas5", verbose=T) background correction: mas normalization: constant PM/MM correction : mas expression values: mas5 background correcting...done. normalizing...Error in list.files(path, pattern, all.files, full.names, recursive) : invalid 'directory' argument > traceback() 7: list.files(...) 6: list.celfiles(celfile.path, full.names = TRUE) 5: AllButCelsForReadAffy(..., filenames = filenames, widget = widget, celfile.path = celfile.path, sampleNames = sampleNames, phenoData = phenoData, description = description) 4: ReadAffy(celfile.path = dir) 3: normalize(afbatch, normalize.method) 2: do.call("normalize", c(alist(afbatch, normalize.method), normalize.param)) 1: expresso(AB, bgcorrect.method = "mas", normalize.method = "constant", pmcorrect.method = "mas", summary.method = "mas5", verbose = T) Any ideas? Thanks, Eric Kort Van Andel Research Institute Grand Rapids, MI USA This email message, including any attachments, is for the\ s...{{dropped}}