Statistical methods on detecting differentially expressed genes for RNA-seq data

BMC Systems Biology

Table 2 Estimated size and power (each condition has three replicates).

Lambda1	Lambda1	LRT	Cond	Wald	Wald-Log	VST	Fisher
5	5	0.0012	0.0009	0.0009	0.0027	0.0012	0.0009
	7	0.0102	0.0062	0.0077	0.0175	0.0103	0.0062
	9	0.0786	0.0542	0.0652	0.1150	0.0786	0.0542
	11	0.2517	0.2008	0.2265	0.3160	0.2517	0.2008
	13	0.5204	0.4581	0.4940	0.5872	0.5204	0.4581
10	10	0.0008	0.0002	0.0006	0.0016	0.0008	0.0002
	12	0.0045	0.0029	0.0042	0.0065	0.0045	0.0029
	14	0.0316	0.0229	0.0279	0.0389	0.0316	0.0229
	16	0.1100	0.0882	0.1019	0.1272	0.1100	0.0882
	18	0.2602	0.2198	0.2454	0.2883	0.2603	0.2198
	20	0.4670	0.4210	0.4515	0.5005	0.4672	0.4210
15	15	0.0007	0.0003	0.0007	0.0007	0.0007	0.0003
	17	0.0034	0.0026	0.0031	0.0049	0.0034	0.0026
	19	0.0181	0.0144	0.0172	0.0221	0.0182	0.0144
	21	0.0612	0.0505	0.0583	0.0712	0.0618	0.0505
	23	0.1442	0.1251	0.1395	0.1648	0.1460	0.1251
	25	0.2850	0.2564	0.2759	0.3125	0.2869	0.2564
30	30	0.0014	0.0010	0.0013	0.0016	0.0014	0.0010
	34	0.0074	0.0057	0.0071	0.0082	0.0074	0.0057
	38	0.0520	0.0457	0.0505	0.0570	0.0520	0.0457
	42	0.2073	0.1846	0.2034	0.2210	0.2073	0.1846
	46	0.4543	0.4270	0.4486	0.4701	0.4543	0.4270

Estimated size and power from each method for detecting the difference of means between two Poisson distributions. There are three replicates for each condition. The Poisson means for the first condition are 5, 10, 15, or 30. The second Poisson means are the same as (for size) or larger than (for power) the first ones. The nominal size (significance level) is 10^-3 and 10,000 runs are used for each setting.

ISSN: 1752-0509