[BioC] MAS5 and Loess normalization

[Arne.Muller at aventis.com]

Hello,

I was wondering if anybody in this group can report experience with the combination of mas5 with Loess normalization for affy chips (in expresso: using mas for bgcorrect, pmcorrect and summary, and loess for the normalization). My data set contains two factors and 3 technical replicates. One factor seems to be very strong (lots of effect) whereas the other is rather weak.

	thanks for any advice,
	+regards,	

	Arne