Table 1.

Average AUC values for simulation data with replicates

PG1	33 %	50 %	50 %	60 %	60 %	70 %	80 %
PG2	33 %	30 %	40 %	20 %	30 %	20 %	10 %
PG3	33 %	20 %	10 %	20 %	10 %	10 %	10 %
(a) PDEG = 5 %
EEE-E (TCC)	91.57	91.50	91.50	91.43	91.42	91.45	91.46
DDD-D (TCC)	90.70	90.62	90.64	90.54	90.55	90.59	90.62
SSS-S (TCC)	88.34	88.33	88.30	88.24	88.23	88.21	88.30
E-E (edgeR)	91.58	91.48	91.47	91.38	91.37	91.38	91.34
edgeR_robust	90.95	90.86	90.85	90.75	90.74	90.74	90.73
D-D (DESeq)	90.71	90.60	90.60	90.50	90.49	90.50	90.48
S-S (DESeq2)	88.34	88.31	88.26	88.19	88.17	88.11	88.14
voom	87.16	87.01	86.99	86.88	86.91	86.88	86.86
SAMseq	85.04	84.97	84.93	84.83	84.88	84.88	84.91
PoissonSeq	87.31	87.25	87.25	87.19	87.17	87.22	87.23
baySeq	90.24	90.21	90.21	90.22	90.17	90.13	90.07
EBSeq	85.77	85.85	85.78	85.81	85.73	85.71	85.77
(b) PDEG = 25 %
EEE-E (TCC)	91.47	91.46	91.45	91.45	91.43	91.42	91.37
DDD-D (TCC)	90.77	90.73	90.72	90.70	90.68	90.65	90.57
SSS-S (TCC)	88.13	88.11	88.13	88.14	88.12	88.09	88.06
E-E (edgeR)	91.47	91.30	91.18	91.06	90.98	90.62	89.97
edgeR_robust	90.89	90.69	90.57	90.43	90.34	89.97	89.27
D-D (DESeq)	90.77	90.54	90.37	90.25	90.15	89.73	89.04
S-S (DESeq2)	88.12	87.83	87.62	87.49	87.36	86.79	85.92
voom	87.08	86.71	86.52	86.29	86.18	85.60	84.56
SAMseq	84.95	84.82	84.82	84.77	84.75	84.72	84.63
PoissonSeq	87.22	87.18	87.14	87.13	87.11	87.06	86.97
baySeq	90.34	90.13	90.07	89.92	89.83	89.52	88.86
EBSeq	85.82	85.61	85.49	85.34	85.30	84.74	84.02

Average AUC values (%) of 100 trials for each simulation condition are shown: (a) P_DEG = 5 % and (b) P_DEG = 25 %. Simulation data contain a total of 10,000 genes: P_DEG % of genes is for DEGs, P_G1 % of P_DEG in G1 is higher than in the other groups, and each group has three BRs (Nrep = 3). Seven conditions are shown in total. The highest AUC value for each condition is in bold