[BioC] overall p-value for multilevel factor in 2 way ANOVA

James W. MacDonald jmacdon at med.umich.edu
Wed Jul 22 15:03:02 CEST 2009

Hi Bernard,

bernard north wrote:
> Dear Bioconductor
> if I had a 2 way ANOVA to analyse, say gender and treatment, where
> treatment had 3 or more levels (eg placebo, drug1 and drug2)
> would there be anu way using the limma output object of obtaining the
> overall p-value for an effect of treatment (as you'd get from an
> ANOVA table as an F statistic with 2 df )- or can we only obtain
> p-values for contrasts eg each drug vs placebo

Have you read the limma User's Guide? I believe section 8.7 is directly 
concerned with this issue.



> many thanks in advance
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618

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