Since GEMMA provides exact computations in essentially the same time as EMMAX, the accuracy of the approximations in EMMAX and other methods may seem moot. However, in some settings, and specifically for mixed models with more than one random effect (variance component), the computational trick used by GEMMA does not apply, and approximations along the lines of EMMAX may remain necessary. For this reason the accuracy of different approximation methods remains of some potential interest, and so we present a comparison between the (Wald test) p values from GEMMA, EMMAX and GRAMMAR, genome-wide, on both the HMDP and WTCCC data sets above.
