Table 3. False-positive rate (FPR) analysis for human ES cells (H3K27me3 data from ENCODE Broad database) for the two replicates.
unit-mean | quantile | MACS | ChIPDiff | rank | RSEG | two-stageunit-mean | ChIPnorm | |
thresholds | p-val | cdf | ||||||
FPR | 0.3924 | 0.0004902 | 0.0053 | 0 | 8.2753 | 0.4845 | 0.8652 | 0.0088 |
We see the percentage of false positive using various methods. Experiments: unit-mean; quantile; MACS peak finder; ChIPDiff; Rank normalization; two-stage unit-mean; ChIPnorm. The thresholds used are same as those in Table 2.