An evaluation of statistical methods for DNA methylation microarray data analysis

BMC Bioinformatics

Table 8 Standard deviation of total discoveries across six DNA methylation differential analysis methods using β 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	3.51	0	0	0.57	4.94	4.94
	0.05	0	3.36	0	0	0.87	5.08	5.08
	0.10	0	3.48	0	0	0.00	5.01	5.01
	0.25	0	3.55	0	0	0.56	5.36	5.37
	0.50	0	4.17	0	0	1.71	6.30	6.43
	0.75	0	4.41	0	0	3.45	6.38	7.03
	0.90	0	4.74	0	0	5.00	7.04	8.05
6	0.01	0.00	0.70	0.00	0.00	0.41	1.26	1.26
	0.05	0.00	0.77	0.00	0.00	1.19	1.47	1.50
	0.10	0.00	0.72	0.00	0.00	2.26	1.68	1.73
	0.25	0.00	1.16	0.00	0.00	6.00	2.93	3.33
	0.50	0.00	2.32	0.00	0.00	12.26	5.89	9.53
	0.75	0.00	6.88	0.00	0.00	17.56	10.06	27.22
	0.90	1.94	17.78	1.94	1.97	20.27	13.17	51.04
12	0.01	0.51	0.94	0.29	0.00	1.07	1.06	1.11
	0.05	1.62	2.79	0.99	0.00	3.48	2.96	3.07
	0.10	4.32	5.61	2.48	0.63	5.38	5.74	6.06
	0.25	12.32	10.81	14.19	15.07	9.15	10.80	12.37
	0.50	13.79	15.16	51.68	17.03	13.59	15.14	20.58
	0.75	31.06	18.20	11.72	19.36	15.82	18.11	32.88
	0.90	19.40	19.47	13.90	20.84	17.52	19.47	44.66
24	0.01	1.66	1.62	1.67	0.00	1.35	1.62	1.62
	0.05	4.68	3.77	6.71	10.98	3.44	3.78	3.86
	0.10	6.50	5.31	6.31	5.09	4.91	5.32	5.47
	0.25	9.92	7.98	7.73	8.23	7.62	8.01	9.26
	0.50	12.56	10.37	7.95	10.64	10.00	10.40	14.80
	0.75	12.78	11.00	6.64	11.17	10.69	11.00	24.48
	0.90	14.06	12.13	7.07	12.19	11.78	12.13	30.75

ISSN: 1471-2105