[BioC] limma contrast matrix interaction effect

Gordon K Smyth smyth at wehi.EDU.AU
Fri Mar 7 00:20:50 CET 2014

Dear Steven,

> Date: Wed, 5 Mar 2014 13:42:34 +0100
> From: steven wink <hardervidertsie at gmail.com>
> To: <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] limma contrast matrix interaction effect
> Dear list,
> I was hoping for some input since I have difficulty figuring out if I
> obtain a valid DEG for my biological question.
> By following the limmaUsersGuide manual I came up with a modification that
> might be suitable for my analysis.
> I have 4 treatments: control, A, B and AB
> so AB is a combined treatment of  A and  B
> After defining my design matrix I set up contrasts:
> SynergisticEffect =  (AB - control ) - ((A - control) + (B - control))
> Would this contrast give me a DEG where I want to test if the combined
> treatment has more effect than the sum of individual treatments?

It would be correct if you changed the "+" to "-".

> Would I first have to test for main effects before stating significant 
> interaction effects? Does this in effect mean I should remove genes from 
> DEG obtained from interaction test that are also in DEG of main effects 
> (ie A-control or B-control and also AB-control)?

No, there is no need whatsoever to do this.

Best wishes

> Any help on making this more clear for me is greatly appreciated!
> Best regards,
> Steven

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