[BioC] Two way ANOVA with bioconductor.

[Alex F. Bokov]

Wow, that was fast! Thanks for your answer.

rossini-at-blindglobe.net (A.J. Rossini) |bioconductor.org| wrote:

> It would be good to be clear -- ANOVA at the gene level, or are you
> thinking of mixing in experiment-level parameters?   For the former,
> Biobase would suffice, though other packages (limma, nlme) might be
> useful as well.  This assumes that you've already got normalized data
> (or else you'd need the appropriate packages)

It's a two-way experiment. Young vs. old, mutant vs. wildtype, with 8 to 10 replicate arrays in each of the four possible combinations. Would that mean it's experiment-level or gene-level (sorry, I don't yet know the proper terminology)?

The sort of thing that in SAS would involve PROC GLM... except the data is probably not normally distributed even after log2 (thus necessitating the empirical null distribution) and of course the multiple comparison problem (thus necessitating multtest or qvalue).

I'm surprised that a two-way ANOVA using an empirical null dist and then adjusted p-values isn't the default analysis everyone does on their microarrays... could it be that everyone in the field is doing t-test style comparisons only?

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