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Figure 3 | BMC Bioinformatics

Figure 3

From: Is this the right normalization? A diagnostic tool for ChIP-seq normalization

Figure 3

Diagnostic plots for simulated data. Diagnostic plots for four simulated datasets, generated from the control sample of the ChIP-seq study by [37]. Figures (a) and (b) are the results from the Read-add simulation, with down-sampling by 2 and 50, respectively. Figures (c) and (d) are the results from the By-Genes simulation, with down-sampling by 2 and 20. The five densities are: the density of \(\log \frac {\tilde {N}_{\textit {ch}} (i)}{\tilde {N}_{\textit {in}} (i)}\) in all bins (solid black curve), the density of the subset of bins in last quartile in length (two-dashed pink), the density of the subset of bins in third quartile in length (dashed blue), the density of the subset of bins in second quartile in length (dot-dashed green), and the density of the subset of bins in first quartile in length (dotted red). The vertical lines show the estimated logr using CisGenome (brown line), CCAT (deepink line) and NCIS (navy line), as well as the true normalization factor in gray. The plot was produced with K=500.

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