[BioC] anova and multiple comparisons

[Kimpel, Mark W]

I have been using SAM to estimate FDR when performing multiple
comparisons on two groups. I have now been tasked with performing a
similar analysis on a 2X2 experiment (2 groups each with two
treatments). For a single comparison, ANOVA would be the obvious choice.
What should be my approach for multiple (about a thousand) comparisons?

Thanks,

Mark W. Kimpel MD

 

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