My experimental design includes 3 discrete factors: diagnosis with two levels (A, B); genotype with two levels (G, T); gender (F, M)

So I can get 8 classes: AGF, AGM, ATF,ATM, BGF, BGM, BTF, BTM. Then I want to perform 2 (diagnosis)* 2(genotype) interaction analysis with regressing out the effect of gender, the contrast matrix is:

0.25  0.25  -0.25  -0.25  -0.25  -0.25  0.25  0.25 

so I can get the clusters that have significant interaction. When I perform the main effect of dignosis, is the following matrix used correct?

0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 (I think it regressed out the effect of genotype and gender, that is take the genotype as a covariable)

 

Or I  should create another fsgd file, that has 4 classes: AF, AM, BF, BM. And I can use the matrix (0.5 0.5 -0.5 -0.5) to perform the main effect of diagnosis. Am I correct? 

Any help will be very appreciated.

 

Best wishes,

 

Meng Li