Hi professor,

Thanks for your reply.

When I perform the main effect of dignosis, is the following  matrix I used correct?
 0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0  (I think it regressed out the effect of genotype and gender, that is it takes 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 0 0 0 0 0 0 0 0) to perform the main effect of diagnosis.

 Which one of two mentioned matrix is right?

 

Thanks a lot.

 

Best wishes

 

Meng