[BioC] post-hoc test after F-test in Limma

[James W. MacDonald]

Hi Christina,

On 8/26/2010 10:12 AM, Christina Orsmark-Pietras wrote:
> Dear List,
>
>
>
> I have computed an F-test on my affy chips in limma comparing 3 groups with
> 20 samples in each group e.g. ctrl, MA, SA. I get the following list with F
> statistics and p value : e.g.
>

In addition to contrasts (as Naomi already mentioned), you could also 
use decideTests() with the 'nestedF' method.

Best,

Jim


>
>
>
>
> ID
>
> MA...Ctrl
>
> SA,,,MA
>
> SA,,,Ctrl
>
> AveExpr
>
> F
>
> P,Value
>
> adj,P,Val
>
>
> 8157727
>
> 0,682329
>
> 0,281631
>
> 0,963959
>
> 6,45911
>
> 29,06583
>
> 1,69E-09
>
> 3,21E-05
>
> 	
>
>
>
>
> My question is how can I get hold on the information on which of the
> contrast/-s is contributing to the significance? As it is now I only know
> that my list of significant genes are diff exp in any of the contrasts.
>
>
>
> Others that have performed similar experiments have used anova and a
> post-hoc test but I have not been able to find how one should perform a
> post-hoc test after limmas F-test.
>
>
>
> Many thanks,
>
> Christina
>
>
>
>
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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