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. 2012 Aug 3;7(8):e39573. doi: 10.1371/journal.pone.0039573

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 Inline graphic Inline graphic p-val Inline graphic Inline graphic Inline graphic cdf Inline graphic Inline graphic Inline graphic
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.