[BioC] Names of the samples(CEl file)(2)

James MacDonald jmacdon at med.umich.edu
Fri May 7 14:48:18 CEST 2004

You have to list the actual celfile names, not what you want to call
them. In addition, you cannot use the widget *and* list the filenames.
If you simply want all the cel files in the directory, try this:

data.test <- ReadAffy(filenames=list.celfiles())

If you only want a subset, you can call list.celfiles() separately and
then subset in the call to ReadAffy()

filenames <- list.celfiles()
data.test <- ReadAffy(filenames=filenames[some subset])

If you really want to use the widget, you can always change the
sampleNames after the fact:

sampleNames(data.test) <- sub("^C:/Program Files/R/rw1090/rdata/","",



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> "Vitalina Komashko" <vmkomashko at bionet.nsc.ru> 05/07/04 07:04AM
Good morning,
I'm still having problems with the sampleNames for my CEL files. I have
already tried to indicate the sample names in ReadAffy function but it
does not help:
> nm<-c("sampleA","sampleB","sampleC")
> data.test<-ReadAffy(widget=TRUE,sampleNames=nm)
> sampleNames(data[1])
[1] "C:/Program Files/R/rw1090/rdata/JS1999081101AA.CEL"

Could anybody please help me?


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