Method ρ Total Match F+ F− CPU(s)
MICS 0.01 30.0(0.00) 30.0(0.00) 0.0(0.00) 0.0(0.00) 2.8
0.05 30.0(0.00) 30.0(0.00) 0.0(0.00) 0.0(0.00) 2.8
0.10 30.0(0.00) 30.0(0.00) 0.0(0.00) 0.0(0.00) 2.8
CCAT 0.01 0.0(0.00) 0.0(0.00) 0.0(0.00) 30.0(0.00) 0.7
0.05 28.8(1.23) 28.8(1.23) 0.0(0.00) 1.2(1.23) 0.7
0.10 28.8(1.23) 28.8(1.23) 0.0(0.00) 1.2(1.23) 0.7
MACS 0.01 28.1(1.37) 28.1(1.37) 0.0(0.00) 1.9(1.37) 12.5
0.05 30.5(0.85) 29.9(0.32) 0.6 (0.70) 0.1(0.31) 12.5
0.10 31.1(1.20) 30.0(0.00) 1.1 (1.20) 0.0(0.00) 12.5
PICS 0.01 22.0(1.94) 22.0(1.94) 0.0(0.00) 8.0(1.94) 8.6
0.05 22.3(1.89) 22.3(1.89) 0.0(0.00) 7.7(1.89) 8.6
0.10 22.3(1.89) 22.3(1.89) 0.0(0.00) 7.7(1.89) 8.5
QuEST 29.7(0.48) 29.7(0.48) 0.0 (0.0) 0.3(0.48) 40.0
BayesPeak pp>0.5 34.2(5.77) 30.0(0.00) 4.2 (5.77) 0.0 (0.00) 2965.0
Table 4: Computational results for the 10 simulated datasets, where ρ denotes the cutoff value for region FDR; Total denotes the average number of peak regions identified by the method; Match denotes the average number of true peak regions discovered by the method; F+ denotes the average number of false positives; F− denotes the average number of false negatives. pp denotes the marginal posterior probability for each claimed region by Bayes Peak. The number in the parentheses is the standard error. Since the number of reads in control condition is less than that in ChIP condition for our simulated datasets, QuEST will not provide FDR estimation, where we put (−) for ρ.