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?
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)?

Any help on making this more clear for me is greatly appreciated!

Best regards,
Steven

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