[BioC] expresso dies on list.files

[James W. MacDonald]

Kort, Eric wrote:
> (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="./")

Is this really the calling sequence you are using? The traceback looks 
really strange to me, as there is no reason I know of that ReadAffy() 
should be called directly after normalize(). I wonder if something is 
busted.

You might want to upgrade, as your Rversion is over a year old now, as 
are your BioC packages (or at least they _should_ be - you haven't 
installed new BioC packages in an old R installation, have you?). A 
sessionInfo() would be very helpful here.

Best,

Jim



>>
>>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
> This email message, including any attachments, is for the so...{{dropped}}
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623