Table 3.

Powers across six DNA methylation differential analysis methods using M values for independent case

n	π 1	Power
		Rank test	t-test	KS test	Permutation	Empirical Bayes	Bump hunting BH	Bump hunting q-value
3	0.01	0	0.0051	0	0	0.0438	0.0399	0.0434
	0.05	0	0.0086	0	0	0.1527	0.0488	0.0573
	0.10	0	0.0126	0	0	0.2905	0.0848	0.1079
	0.25	0	0.0331	0	0	0.4927	0.2117	0.3023
	0.50	0	0.1051	0	0	0.6364	0.3702	0.5922
	0.75	0	0.2030	0	0	0.7135	0.4725	0.8386
	0.90	0	0.2633	0	0	0.7445	0.5148	0.9629
6	0.01	0.0000	0.2307	0.0000	0.0000	0.5442	0.3903	0.4004
	0.05	0.0000	0.4511	0.0000	0.0000	0.6911	0.5977	0.6131
	0.10	0.5894	0.5699	0.5894	0.5894	0.7561	0.6913	0.7140
	0.25	0.6640	0.7182	0.5926	0.7072	0.8352	0.8014	0.8476
	0.50	0.7263	0.8083	0.5919	0.8215	0.8876	0.8609	0.9450
	0.75	0.7865	0.8508	0.8654	0.8596	0.9133	0.8838	0.9964
	0.90	0.7875	0.8689	0.8666	0.8778	0.9254	0.8920	0.9999
12	0.01	0.7541	0.7896	0.8053	0.0000	0.8317	0.8475	0.8520
	0.05	0.8722	0.8956	0.9179	0.8910	0.9151	0.9447	0.9499
	0.10	0.9082	0.9224	0.9164	0.9240	0.9379	0.9682	0.9751
	0.25	0.9423	0.9535	0.9672	0.9565	0.9649	0.9890	0.9973
	0.50	0.9643	0.9708	0.9674	0.9730	0.9791	0.9944	1.0000
	0.75	0.9714	0.9784	0.9893	0.9799	0.9854	0.9919	1.0000
	0.90	0.9753	0.9817	0.9895	0.9829	0.9881	0.9878	1.0000
24	0.01	0.9612	0.9600	0.9875	0.0000	0.9597	0.9754	0.9763
	0.05	0.9883	0.9892	0.9973	0.9861	0.9905	0.9989	0.9990
	0.10	0.9929	0.9937	0.9991	0.9935	0.9946	0.9998	0.9999
	0.25	0.9967	0.9972	0.9997	0.9972	0.9977	1.0000	1.0000
	0.50	0.9982	0.9986	0.9997	0.9986	0.9990	1.0000	1.0000
	0.75	0.9989	0.9992	0.9999	0.9992	0.9994	1.0000	1.0000
	0.90	0.9990	0.9993	0.9999	0.9993	0.9995	1.0000	1.0000