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. 2021 Jan;31(1):131–145. doi: 10.1101/gr.262675.120

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© 2021 Tu et al.; Published by Cold Spring Harbor Laboratory Press

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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Figure 3. — Comparison among empirical Bayes methods that take the mean-variance/dispersion relationship into account. (A) Comparing the performance of MAnorm2 with limma-trend, voom, and DESeq2 in the differential analysis of H3K4me3 ChIP-seq data between GM12891 and GM12892. (B) Comparing the four methods in all pairwise comparisons of H3K4me3 levels among GM12890, GM12891, GM12892, and SNYDER LCLs. Each line corresponds to an individual comparison between two LCLs, and the methods are sorted by the average true discovery proportion (among 500 top-ranked promoter intervals) across all the six comparisons. (C,D) Comparing the four methods with unifying their normalization methods to hierarchical MA normalization. (E,F) Comparing the performance of MAnorm2 coupled with different normalization methods. Note that methods in D and F have been sorted as well.