Table 2.

Bias and variance of FDR estimation: FDR is the estimated true value averaged over 100 simulations, TNR is the total number of rejections. P_t/P_e are p-values derived from the theoretical/empirical null distributions, EB is empirical Bayes ranking with local FDR based on the empirical null distribution. C₀ is based on the 75% quantile.

λ0 = 0, σ0 = 1, λ = 10
TNR	50			100			200
	FDR	bias	stderr	FDR	bias	stderr	FDR	bias	stderr
Pt	0.019	0.003	0.006	0.049	−0.002	0.009	0.119	−0.004	0.017
Pe	0.019	0.006	0.008	0.049	0.004	0.015	0.119	0.008	0.027
EB	0.019	0.006	0.009	0.049	0.004	0.015	0.119	0.009	0.028
λ0 = 0.5, σ0 = 2, λ = 10
TNR	50			100			200
	FDR	bias	stderr	FDR	bias	stderr	FDR	bias	stderr
Pt	0.071	−0.071	0.000	0.118	−0.118	0.000	0.218	−0.217	0.0001
Pe	0.071	0.013	0.041	0.118	0.020	0.057	0.218	0.027	0.083
EB	0.071	0.013	0.041	0.118	0.021	0.058	0.218	0.028	0.084
λ0 = 0.5, σ0 = 0.5, λ = 10
TNR	50			100			200
	FDR	bias	stderr	FDR	bias	stderr	FDR	bias	stderr
Pt	0.078	0.903	0.042	0.130	0.870	0.0001	0.224	0.776	0.0001
Pe	0.078	0.001	0.047	0.130	0.005	0.068	0.224	0.013	0.092
EB	0.077	0.001	0.047	0.130	0.005	0.068	0.224	0.014	0.093