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

Table 2. Sensitivity analysis for human ES and GM12878 cells (replicate 1 data from ENCODE Broad database) percentages using various methods.

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
GM12878 differential (four-fold) expressed: 1927 genes
sensitivity (HES K27-enriched) 11.26 11.26 11.26 10.85 17.85 8.27 10.69 11.05
error (GM12878 K27-enriched) 0.10 0.21 0 0.16 5.35 0 0.31 0.16
HES differential (four-fold) expressed: 2908 genes
sensitivity (GM12878 K27-enriched) 1.55 10.97 1.79 4.09 33.29 0.06 14.65 12.00
error (HES K27-enriched) 1.38 0.93 3.54 1.20 2.27 11.81 1.20 0.55

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