Table 5.

Standard deviation of total discoveries across six DNA methylation differentially analysis methods using M values for independent case

n	π 1	Standard deviation of total discoveries
		Rank test	t-test	KS test	Permutation	Empirical Bayes	Bump hunting BH	Bump hunting q-value
3	0.01	0	0.33	0	0	0.80	0.82	0.85
	0.05	0	0.92	0	0	4.66	2.64	2.95
	0.10	0	1.84	0	0	7.57	5.55	6.60
	0.25	0	6.64	0	0	10.79	12.82	15.70
	0.50	0	18.85	0	0	13.92	18.93	26.01
	0.75	0	27.87	0	0	15.81	21.28	38.30
	0.90	0	29.67	0	0	15.80	21.35	43.19
6	0.01	0.00	1.70	0.00	0.00	1.41	1.94	1.95
	0.05	0.00	4.61	0.00	0.00	3.19	4.20	4.26
	0.10	4.44	5.83	4.44	4.44	4.36	5.34	5.51
	0.25	12.17	8.01	7.04	8.71	6.60	7.46	8.47
	0.50	9.47	9.98	9.73	9.70	8.08	8.92	12.08
	0.75	9.90	10.02	8.55	10.46	8.23	9.28	18.02
	0.90	10.73	9.97	9.10	9.23	7.90	9.27	23.71
12	0.01	1.41	1.18	1.02	0.00	1.13	1.22	1.23
	0.05	3.01	2.36	2.14	2.35	2.39	2.45	2.51
	0.10	3.32	3.24	2.66	3.83	3.24	3.25	3.42
	0.25	5.26	4.36	3.65	4.26	4.58	4.40	5.20
	0.50	5.16	5.01	4.28	5.23	5.12	4.99	8.04
	0.75	5.07	4.80	3.83	4.88	4.75	4.74	12.59
	0.90	5.51	4.33	3.46	4.22	3.96	4.27	18.66
24	0.01	0.96	0.87	0.71	0.00	0.96	0.91	0.92
	0.05	1.86	1.72	1.23	1.63	1.82	1.75	1.84
	0.10	2.42	2.36	1.99	2.35	2.46	2.43	2.71
	0.25	3.21	3.18	2.92	3.50	3.40	3.22	4.09
	0.50	3.89	3.67	2.38	3.79	4.11	3.71	7.08
	0.75	2.99	3.04	2.57	3.14	3.37	3.07	11.45
	0.90	2.25	2.30	1.77	2.36	2.59	2.30	18.40