[BioC] Multiple testing correction on 2-Way ANOVA

[Liaw, Andy]

I am absolutely no expert in multiple comparison / multiple testing / gene
expression data analysis, so take the following with appropriate dose of
salt:

It really depends on what you are looking to get out of the data.  Just
because you have multi-factor data with > 2 levels and thousands of
responses, it doesn't automatically mean that the usual multiple comparison
procedures are appropriate.  You design the experiment to answer some
specific questions (hopefully).  How you analyze the data depends greatly on
what those questions are, and (hopefully, therefore) how the experiment is
designed.

Best,
Andy

> From: Eric
> 
> Hi,
> 
> I apologize for this being off-topic- it's really a 
> statistical question 
> but I'd be interested in the community's input. If I run a 
> 'per gene' 2-way 
> ANOVA on single channel microarray data (i.e., each gene is tested 
> separately by 2-Way ANOVA), should I run multiple testing 
> correction for 
> each factor and interaction separately? Alternatively, should 
> I use an 
> overall (omnibus) F-test, correct that for multiple testing, 
> and treat the 
> main effects and interaction results as post-hoc to the overall test?
> 
> Thanks,
> -E
> 
> Eric Blalock, PhD
> Dept Pharmacology, UKMC
> 859 323-8033
> 
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