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Omar, Since your models are different, they will give a different result. This is not a surprise. There are several differences/potential differences: (1) In the t-test, you assumed that the effect of diagnosis had the same effect for both genotypes (1 covariate); (2) In the t-test, you might not have set the variance to unequal; (3) Differences in the design matrix leads to different degrees of freedom and a different residual error. As has been said before on the list. You first need to develop your research question and then select the model that will best answer the question. Without knowing your question, its hard to assess which model would be better. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Mon, Jun 25, 2012 at 5:49 AM, Omar Mothersill <[log in to unmask]> wrote: > Dear SPM users, > > In SPM 8, I used an independent t-test to compare two genotype groups on a > task, and I included a categorical covariate (control or patient) in the > model. As an alternative, I also tried a full factorial with two factors, > diagnosis and genotype. However, these tests give completely different > results, and I'm not sure why. I set the full factorial as follows: > > Factor 1 (genotype): > Levels - 2 > Independence - Yes > Variance - Unequal > > Factor 2 (diagnosis): > Levels - 2 > Independence - Yes > Variance - Unequal > > If anyone has any advice it would be greatly appreciated. I've also > included the design matrix for the full factorial model, perhaps there is a > problem with it? > > Kind regards, > > Omar Mothersill > > > -- > Omar Mothersill > > Room 0.18 > Neuropsychiatric Genetics Group > Dept. of Psychiatry > Trinity Centre for Health Sciences > St. James's Hospital > Dublin 8. > > Phone: 01 896 2464 > Email: [log in to unmask] > >