[BioC] expresso still dying on list.files()--solved

[Kort, Eric]

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 at 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
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