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

[Naomi Altman]

Usually you would do pair-wise comparisons using contrasts.  Or did 
you have something else in mind?

--Naomi

At 10:12 AM 8/26/2010, 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.
>
>
>
>
>
>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
>
>
>
>
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>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111