An evaluation of statistical methods for DNA methylation microarray data analysis

BMC Bioinformatics

Table 9 Standard deviation of total discoveries across six DNA methylation differentially analysis methods using M values for correlated 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	0.30	0	0.00	0.22	0.76	0.88
	0.05	0	0.45	0	0.03	0.19	0.90	1.04
	0.10	0	0.67	0	0.00	0.26	1.35	1.61
	0.25	0	1.00	0	0.04	0.36	2.00	2.48
	0.50	0	1.56	0	0.03	0.62	2.93	4.13
	0.75	0	2.13	0	0.03	0.85	3.82	6.21
	0.90	0	2.48	0	0.03	1.18	4.46	38.95
6	0.01	0.00	0.08	0.00	0.00	0.14	0.21	0.21
	0.05	0.00	0.14	0.00	0.00	0.11	0.26	0.29
	0.10	0.00	0.17	0.00	0.00	0.14	0.29	0.31
	0.25	0.00	0.27	0.00	0.00	0.25	0.48	0.55
	0.50	0.00	0.39	0.00	0.00	0.36	0.67	0.96
	0.75	0.00	0.49	0.00	0.00	0.59	0.83	119.14
	0.90	1.94	0.54	1.94	1.97	0.91	0.98	166.82
12	0.01	0.50	0.06	0.29	0.00	0.16	0.12	0.13
	0.05	1.61	0.11	0.98	0.00	0.23	0.32	0.36
	0.10	4.29	0.16	2.47	10.35	0.35	0.52	0.60
	0.25	12.39	0.36	14.19	12.94	0.99	1.71	4.88
	0.50	13.82	0.68	51.43	14.47	13.96	15.04	56.63
	0.75	31.13	2.07	11.71	15.66	41.52	51.51	41.62
	0.90	19.59	4.98	14.03	16.74	33.38	43.90	27.44
24	0.01	1.65	0.83	1.67	0.00	0.89	1.24	1.28
	0.05	4.72	5.14	6.69	5.33	4.23	5.56	5.81
	0.10	6.54	8.72	6.29	4.82	8.17	7.44	7.95
	0.25	9.91	9.78	7.74	6.07	9.53	8.87	10.16
	0.50	12.61	9.43	7.97	6.60	9.63	8.78	11.47
	0.75	12.79	8.51	6.67	6.12	8.20	8.19	13.85
	0.90	14.08	7.87	7.14	5.77	7.84	7.81	20.16

ISSN: 1471-2105