I am having some difficulty defining the correct contrast to test for synergy of two treatments A & B vs AB using the deseq2 results function. Treatment has 4 levels A, B, combined AB and reference level control.
When I set up contrasts e.g.
( AB - control ) - [(A - control) + (B - control)] I end up with
AB - A - B + control! How can I get rid of the double counted control here? What am I missing?
My design is
~ donor + condition + treatment + treatment:condition
Thanks in advance for your time.