[BioC] (no subject)

[Kort, Eric]

Hello.  I am running 64 bit R 2.0.1 on SUSE Linux, and despite
successful use in the past, I have been recently been unable to
normalize some affy data using expresso.  I receive an error with
list.files that I can not figure out.  While list.files seems to
generate the error below, if I explicitly call "list.files("./"), I
receive no error.

Here is my code and the resulting error and traceback:

>AB <- ReadAffy(celfile.path="./")
>
>eset <- expresso(AB, bgcorrect.method="mas",
normalize.method="constant",
+ pmcorrect.method="mas", summary.method="mas", verbose=T)
background correction: mas
normalization: constant
PM/MM correction : mas
expression values: mas
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 = "mas", verbose = T)


Can someone tell me why this is not working?

Thank you,

Eric Kort
Van Andel Research Institute
Grand Rapids, MI 49503 
USA
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