[BioC] another kooperberg question

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Wed Sep 14 17:52:55 CEST 2005

Hi Matt

Hmmmm, something like this *should* work:

# read in the data normally just to get the weights
RG <- read.maimages(targets$FileName, source="genepix", wt.fun=filters)

# read in the data using read.series and EXACTLT THE SAME DATA FILES as
# ...
Rgmodel <- kooperberg(RG, fg="mean", bg="median", a=TRUE,

# transfer the weights from RG to Rgmodel
Rgmodel$weights <- RG$weights

I think....


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of
scholz at Ag.arizona.edu
Sent: 12 September 2005 10:59
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] another kooperberg question

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

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