[BioC] limma contrast matrix interaction effect

Gordon K Smyth smyth at wehi.EDU.AU
Sat Mar 8 07:30:24 CET 2014

On Fri, 7 Mar 2014, steven wink wrote:

> Did you notice the double brackets? SynergisticEffect =  (AB - control ) -*
> (*(A - control) + (B - control)*)*

Yes, I missed the double brackets.  Your contrast was fine.

> To simplify I should write:  AB + C - A - B instead of  (AB - control )

Yes, as Dario has already suggested.  It makes no difference.  Any 
algebraic equation that is equivalent will give the same result in limma.

> I would like to find significant genes where abs(log2_FC(AB))  >> abs( 
> log2_FC(A) + log2_FC(B) ), where FC is fold change as compared to 
> control (C)

I don't think that this is really what you mean.  Surely you would want to 
find genes for which the AB effect was in a different direction to the A 
and B effects, even it was not greater in absolute value.  The contrast 
does this.  If what you state is really is what you mean, then this is not 
something you can formally test in limma (or an any other statistics 
program afaik).


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