TABLE IV.

Power of the proposed test statistics for Case 3. Here p₁ = p₂ = 4 (the interaction SNPs have been eliminated for the analysis) and we test for equality of the two 4 × 4 blocks Σ₁₂ and Ω₁₂. IM1, multiplicative within and between loci – no interaction; IM2, multiplicative model and no main effects; IM3, the threshold model. For this set of simulations, 1000 cases and 1000 controls were sampled for each of 1000 simulation runs. We completed 10000 permutations for each data set, and controlled the significance level at α = 0.05.

		Parameter β in the model
		0	0.1	0.5	1	2	4
IM1	δ2	0.048	0.049	0.050	0.051	0.052	0.052
	LM1	0.047	0.049	0.049	0.051	0.052	0.052
	LM2	0.048	0.048	0.051	0.050	0.051	0.053
IM2	δ2	0.047	0.061	0.089	0.155	0.465	1.000
	LM1	0.049	0.054	0.060	0.084	0.226	0.685
	LM2	0.049	0.055	0.065	0.099	0.242	0.721
IM3	δ2	0.049	0.059	0.068	0.105	0.235	0.611
	LM1	0.049	0.050	0.054	0.061	0.067	0.128
	LM2	0.049	0.050	0.055	0.069	0.076	0.141