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
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422
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