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

Table 1. Sensitivity analysis percentages using various methods (data from Mikkelsen et al. 2007 [8]).

unit-mean quantile MACS ChIPDiff rank RSEG two-stage unit-mean ChIPnorm
thresholds Inline graphic Inline graphic p-val Inline graphic Inline graphic Inline graphic cdf Inline graphic Inline graphic Inline graphic
NP differential (four-fold) expressed: 925 genes
sensitivity (ES K27-enriched) 14.49 15.24 31.24 14.64 17.62 18.16 15.14 15.14
error (NP K27-enriched) 0 0 0 0.27 6.05 0.11 0 0
ES differential (four-fold) expressed: 1104 genes
sensitivity (NP K27-enriched) 0 1.27 0.27 0 12.59 1.9 6.88 7.16
error (ES K27-enriched) 1.27 1.99 5.07 0.91 5.43 3.08 1.18 1.99

Experiments: unit-mean; quantile; MACS peak finder; ChIPDiff; Rank normalization; two-stage unit-mean; ChIPnorm. The parameters of all the methods (except MACS) were adjusted so that all of them give almost the same percentage (Inline graphic) of experiment “sensitivity (ES K27-enriched)”.