[BioC] another kooperberg question

[scholz@Ag.arizona.edu]

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?

Thanks

Matt 
scholz at ag.arizona.edu
 

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