Extended Data Fig. 7: FDR determined by Bayes Factor vs. ANOVA analysis. | Nature Genetics

Extended Data Fig. 7: FDR determined by Bayes Factor vs. ANOVA analysis.

From: Discovering functional evolutionary dependencies in human cancers

Extended Data Fig. 7

a) Example of synthetic positive (P) and negative (N) cases generated to mimic the real-case scenarios (as in panel B). Extensive sets of multiple synthetic P and N cases were generated, with different combinations of Dp, Np, and Nn parameters. Dp: the difference between the mean parameters of the normal distributions from which phenotype values for the samples in the red and purple classes are drawn. Np and Nn: the number of samples in red and purple classes, for positive (P) and negative (N) cases, respectively. The synthetic dataset was used to assess and compare the ANOVA and Bayesian inference frameworks. Boxplots in this panel are used as symbolic examples and do not represent actual data. b) True and False Positive rates for direct and indirect post-hoc tests, for synthetic sets of P and N cases with different effect sizes (Dp) and same number of P and N samples (Np = Nn). c) True and False Positive rates for direct and indirect post-hoc tests, for more extreme cases with small effect size (Dp) and lower number of P samples (Np << Nn). d) True and False Positive rates (left panel) and FDR (right panel) for synthetic sets of P and N cases with small effect size (Dp) and lower number of P samples (Np << Nn). The thick central line of each box plot in all panels, with the exception of panel e, represents the median number of significant motifs, the bounding box corresponds to the 25th–75th percentiles and the whiskers extend up to 1.5 times the interquartile range. The data in these boxplots are randomly drawn from normal distributions and do not represent actual data.

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