Figure 2.

Computational experiments comparing jMOSAiCS with the separate analysis approach on data simulated from the STAT1 ChIP-seq experiment. jMOSAiCS-B, jMOSAiCS-E1, and jMOSAiCS-E2 are results derived from posterior probability inferences of the B, E1, and E2 variables. Separate-B, Separate-E1, and Separate-E2 are results derived from separate analysis of each dataset. (a) Proportion of top ranking enriched regions that are true positives. (b) Sensitivity by nominal FDR. (c) Observed FDR by nominal FDR. ChIP: chromatin immunoprecipitation; FDR: false discovery rate; jMOSAiCS: joint model-based one- and two-sample analysis and inference for ChIP-seq

Zeng et al. Genome Biology 2013 14:R38   doi:10.1186/gb-2013-14-4-r38
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