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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