I think that you misunderstood me.
As far as I know, RMA does three things: background correction,
quantile normalization, and summary from probes to probesets. I want
the probe values after background correction and quantile
normalization but before the summary.
On Sat, Dec 26, 2009 at 12:07
You'll need to use calls to bg.correct and the other functions in
sequence and save the probe values along the way.
See the example in ?normalize.AffyBatch.normalize2Reference in the
caret package.
Also, don't email R help about this. Keep it on the bioC mailing list.
Max
On Sat, Dec 26, 2009
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