TABLE 2.

Estimated Type I error rates for tests of G × E interaction across several parameter settings for a continuously-measured genes (Section 3.2). Each estimate of Type I error is based on the proportion of 10,000 replicate datasets for which the indicated procedure identified at least one statistically significant result (at the 0.05 level) among the 𝑀 = 10,000 genes. For the subset screening step, a filtering statistic of α₁ = 0.05 was used. For the weighted Bonferroni test, an initial bin size of B = 5 was used. See Section 3.2 for details on the simulation settings. The Base Model corresponds to the following simulation parameters: γ = (0,log(0.6),0), π_E = 0.5, event rate ≈ 40−44%, Σ_X = I_P, N = 1,000. AR(ᵨ) corresponds to an autoregressive correlation structure with correlation parameter ᵨ.

	Standard	Two-Step Methods
		mG|𝐺 × 𝐸		cG|𝐺 × 𝐸
	GWIS	Subset	Weighted	Subset	Weighted
Base Model	0.048	0.084	0.107	0.050	0.047
γE = log(1)	0.051	0.048	0.048	0.049	0.048
γE = log(0.8)	0.046	0.059	0.062	0.051	0.047
γE = log(0.4)	0.051	0.130	0.175	0.052	0.053
γG = log(0.8); 𝛾𝐸 = log(0.8)	0.048	0.057	0.064	0.051	0.054
γG = log(0.8); γE = log(0.6)	0.046	0.080	0.097	0.051	0.052
γG = log(0.6); γE = log(0.8)	0.051	0.056	0.056	0.052	0.052
γG = log(0.6); γE = log(0.6)	0.047	0.070	0.074	0.054	0.049
γG = log(1.2); γE = log(0.6)	0.047	0.083	0.100	0.051	0.051
ΣX = log (0.3)	0.050	0.085	0.108	0.052	0.051
ΣX = log (0.6)	0.054	0.083	0.098	0.054	0.049
πE = 0.4	0.055	0.088	0.102	0.050	0.048
πE = 0.2	0.056	0.074	0.088	0.054	0.052
Event rate ≈ 0.79	0.051	0.108	0.140	0.051	0.052
Event rate ≈ 0.24	0.051	0.059	0.061	0.053	0.050
N = 2,000	0.052	0.084	0.105	0.049	0.049