Figure 3.

Computational experiments comparing jMOSAiCS with the separate analysis approach on data simulated from the MeCP2 ChIP-seq experiment. Comparisons of region level (B) results of jMOSAiCS and separate analysis. jMOSAiCS (x-y) and Separate (x-y) refer to jMOSAiCS and separate analysis of x lanes of replicate 1 with y lanes of replicate 2. (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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