That contrast will do what you want but a more general one would be [1 -1 0 0 0 0 0 0 0 0 0 0] [0 0 0 1 -1 0 0 0 0 0 0 0] [1 0 -1 0 0 0 0 0 0 0 0 0] [0 0 0 1 0 -1 0 0 0 0 0 0]

This will return positive if there is any difference between the genotypes regardless of gender. In your contrast, you could have a situation where the G-A difference is positive for males but negative for females in which case they would cancel each other out.

doug

On 11/13/2012 08:50 AM, xiangbo_2010 wrote: Hi Freesurfer experts,

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,

Bo Xiang