Entering edit mode
(I apologize for sending this query a second time, but I forgot to add
a
descriptive subject last time which I thought may have contributed to
the lack of response.)
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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