[BioC] Affy: present genes and anova

[Arne.Muller at aventis.com]

Hello,

I've been running anova to identify modulated genes of an affy experiment (normalized data).

When only considering those genes with a very confident F-test p-value (<=1e-4) there are hardly any genes found with very low intensities - which is good.

My concern is/was that the anova analysis may pick up absent genes (genes not expressed at all - but for which there's a signal just due to noise). Surely this may happene if the anova p-value is raised.

This is one reason why I'm a bit worried about using RMA since I cannot skip absent genes before I run the anova. Well, I can, but just based on the intensity, since RMA does not provide a p-value for the presence call liske MAS5.

Does anova have the nice side effect to give bad (f-test) p-values to absent genes, because intesities just due to noise should have similar means and varaince in all factor levels?

I'd be interested in your experience and opinion about this.

	kind regads,

	Arne

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