[BioC] scaling normalization between groups

[Karin Lagesen]

Hello

I have four groups a 5 chips each, all Affymetrix chips. I would like
to be able to normalize them separately (within-group) and then see
the scaling factor between them.

I have now got so far that I have four normalized affybatch objects.

> class(mockbgnorm)
[1] "AffyBatch"
attr(,"package")
[1] "affy"
> 

and three more like this one.

I was reading the normalize.AffyBatch.constant docs, and I gather that
if I can make an affybatch object containing for instance all of
mockbgnorm and one chip from the set I am comparing with, I can do
normalize.AffyBatch.constant with the comparison chip as the
reference. However, I am stuck at making this affybatch object.

Can anyone give me any tips on how to best do this? Am I thinking
correctly?

Thanks,

Karin
-- 
Karin Lagesen, PhD student
karin.lagesen at medisin.uio.no
http://folk.uio.no/karinlag