Classical and Bayesian random-effects meta-analysis models with sample quality weights in gene expression studies

BMC Bioinformatics

Table 3 Performance of random-effects models applied in simulated data

Model	Prior	No. DE Genes				MSSE				Precision				Accuracy				AUC
Model	Prior	H0	H1	H2	H3	H0	H1	H2	H3	H0	H1	H2	H3	H0	H1	H2	H3	H0	H1	H2	H3
DSL	–	65	74	92	124	2.9	2.9	2.9	2.9	0.95	0.95	0.91	0.79	0.97	0.97	0.98	0.98	0.76	0.79	0.84	0.90
DSLR2	–	69	104	139	198	1.7	1.7	1.7	1.7	0.95	0.91	0.79	0.59	0.97	0.98	0.98	0.96	0.77	0.89	0.95	0.97
BRE	U(0,0.001)	126	157	254	305	18.1	25.8	33.0	39.9	0.82	0.70	0.45	0.39	0.98	0.97	0.93	0.91	0.93	0.94	0.94	0.94
BRE	U(0,0.01)	218	324	404	436	10.5	16.0	20.0	22.3	0.55	0.37	0.30	0.28	0.95	0.90	0.86	0.84	0.97	0.95	0.92	0.92
BRE	U(0,0.1)	181	269	354	391	9.4	14.3	17.8	19.8	0.66	0.45	0.34	0.31	0.97	0.93	0.88	0.86	0.98	0.96	0.94	0.93
BRE	U(0,1)	80	108	141	203	1.7	2.2	2.4	2.6	1.00	0.94	0.80	0.58	0.98	0.99	0.98	0.96	0.84	0.92	0.96	0.97
BRE	U(0,10)	11	9	9	12	1.0	1.1	1.1	1.1	1.00	1.00	1.00	0.96	0.95	0.94	0.94	0.95	0.54	0.54	0.54	0.55
BRE	U(0,100)	10	8	8	11	1.0	1.0	1.0	1.0	1.00	1.00	1.00	0.96	0.94	0.94	0.94	0.94	0.54	0.53	0.53	0.54
BRE	U(0,0.005)	329	447	520	546	10.6	16.1	20.1	22.4	0.37	0.27	0.23	0.22	0.90	0.84	0.80	0.79	0.94	0.91	0.89	0.89
BRE	U(0,0.05)	184	275	359	395	10.3	15.7	19.6	21.8	0.65	0.44	0.33	0.30	0.97	0.92	0.88	0.86	0.98	0.96	0.94	0.93
BRE	U(0,0.5)	137	167	253	330	3.0	4.4	5.3	5.7	0.86	0.71	0.47	0.36	0.99	0.98	0.93	0.89	0.98	0.98	0.96	0.94
BRE	U(0,5)	13	11	12	17	1.1	1.1	1.1	1.1	1.00	1.00	1.00	0.97	0.95	0.95	0.95	0.95	0.55	0.54	0.55	0.57
BRE	G(1,2)	41	53	69	94	1.7	2.0	2.1	2.1	1.00	1.00	0.97	0.89	0.96	0.97	0.97	0.98	0.67	0.72	0.78	0.84

DE: differentially expressed, MSSE: minimum sum of squared error, AUC: area-under ROC curve, DSL: Dersimonian-Laird model, DSLR2: two-step estimate of Dersimonian-Laird model, BRE: Bayesian random-effects model, U: uniform, and G: gamma. H0, H1, H2, and H3 are the number of {0, 1, 2, and 3} studies containing heterogeneous genes. H0 represents homogenous data. The number of truly DE genes in the simulated data was 120 genes under HSC hypothesis testing

ISSN: 1471-2105