[BioC] Friedman test

[Arne.Muller at aventis.com]

Hello,

I've a rather statistical question ...

I've an experimental design with 2 factors, batch (3 levels) and dose (5 levels) with 0 to 4 technical replicates (a dose is missing for a certain batch). I've seen that one batch has consistently lower variance within doses for most of the genes I've looked at.

I'm performing a 2way anova, and was wondering if this screws up the results, since the assumption of equal variance is violated (quite a lot, I think!).

Does it make sense to "fake" a random block design by taking the mean of the technical replicates and then run a friedman test? I've never used this test before, and I don't realy feel happy taking the means without considering the variance of replicates ...

Any hints and thoughts are appreciated,

	+kind regards,

	Arne