[BioC] another kooperberg question

scholz@Ag.arizona.edu scholz at Ag.arizona.edu
Mon Sep 12 09:58:44 CEST 2005

Hi all,

I'm trying to run the Kooperberg correction on filtered data from genepix files.
I've read my genepix data into and RGList (cleverly named RG) via a wt.fun
function that filters out certain control spots that I don't want thrown into
the analysis. In other words, I did:

RG <- read.maimages(targets$FileName, source="genepix", wt.fun=filters)

I now want to take this filtered data set and run kooperberg on it. The problem
I'm having is that Kooperberg apparently requires a character vector containing
genepix filenames as its initial argument but what I have is an RGList, not a
character vector. In other words, I would like to do something like the following:

> kooperberg(RG, fg="mean", bg="median", a=TRUE, layout=RGlayout)

but RG is not an acceptable "names" argument. Obviously, I can't used the
targets$FileName vector I used to initially read in the RGList because this is
unfiltered data, and I can't use wt.fun within kooperberg. Any ideas on how to
pass filtered data on to kooperberg?


scholz at ag.arizona.edu

College of Agriculture and Life Sciences Web Mail.

More information about the Bioconductor mailing list