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 Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.