[BioC] when to call pmcorrect in affy

[Arne.Muller at aventis.com]

Hello,

when processing an affybatch by performing all steps "manually" (i.e. not using expresso or justRMA), when do I call pmcorret?

does this order make sense?
1. bgcorrect (rma)
2. normalize (quantiles)
3. pmcorrect (pmonly)
 ... no summary!

In this case (since I'm using rma) do I have to take care that I remove the MM intensities from the affybatch before passing the bgcorrected affybatch to the normalization (because on the PMs were corrected)?

Basically I'd just like to skip the last step the "summary" to finally have a matrix with the probe insensities (and not the summarized *probeset* intensities). justMA cannot leave out the summary step, can it?

	kind regards + thanks for your comments,

	Arne

--
Arne Muller, Ph.D.
Toxicogenomics, Aventis Pharma
arne dot muller domain=aventis com