I'm very sorry to bother you, but I am very confused with the following questions:

My experimental design includes two discrete factors:  genotype with three levels (GG,GA,AA ); gender (F, M), and one covariate.

So I can get 6 classes: MGG, MGA,MAA, FGG,FGA,FAA.

1)  I want to perform the difference between any of the genotype leves analysis with regressing out the effect of gender and one covariate, but I don't know the rules for setting the contrasts for the F-test.  The contrast matrix I used is:

[1 -1 0 1 -1 0 0 0 0 0 0 0 ]/2

[1 0 -1 1 0 -1 0 0 0 0 0 0 ]/2 

is it correct?  

 

Any help will be very appreciated.

 

Best wishes,

 

Meng Li