Hello, The results should be very similar. The first question that comes to mind is: are you using the same covariance (relationship) matrix for each software? how did you calculate it? When you say the results are slightly different, could you please elaborate? What is different? and how different is it? I wouldn't expect the numerical solutions to be *exactly *the same seeing as the solution is found through an iterative process, but I would expect them to be quite similar. Matt On Mon, Nov 19, 2018 at 11:24 AM naglemi [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User naglemi <https: support.bioconductor.org="" u="" 16588=""/> wrote Question: > Difference between AssocTestMM (GENESIS) and EMMAX? Why results are > different? <https: support.bioconductor.org="" p="" 115254=""/>: > > I'm trying to figure out what the differences between AssocTestMM (in > GENESIS library) and EMMAX are. I was told they are equivalent, but the > results I'm getting from the two are slightly different. Should they match > perfectly? What is the cause of the differences? > > Thank you. > ------------------------------ > > Post tags: GENESIS, GWAS, AssocTestMM > > You may reply via email or visit > Difference between AssocTestMM (GENESIS) and EMMAX? Why results are different? > -- Matthew P. Conomos, PhD. Research Scientist Department of Biostatistics Genetics Analysis Center University of Washington Seattle, WA 98105-1016, USA email: mconomos@uw.edu phone: (206) 685-8848