[BioC] RMA on PM only

[Arne.Muller at aventis.com]

Hi All,

RMA background correction transforms the expression values by log2, right?

I'm running rma on the PM probes only to get a background corrected and normalized matrix of probes (no summary!). However, the values of that matrix do not seem to be log transformed. My question  is whether I'm doing something wrong here.

this is the protocol:

cel.all <- ReadAffy(filenames=fn)
pm.all <- pm(cel.all)
bgc.all <- apply(pm.all, 2, bg.adjust)
nor.all <- normalize.quantiles(bgc.all)

	kind regards,

	Arne

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