FIGURE 3.

FDP-TPR curves of DE methods on simulated datasets generated by GLMMs with μ_π = 0. (A) Line plot of the FDP-TPR curves for simulated datasets based on NB GLMMs for each of 12 DE methods with the dispersion parameter θ = 0.5. (B) Line plot of the FDP-TPR curves for simulated datasets based on negative binomial (NB) GLMMs for each of 12 DE methods with θ = 1. (C) Line plot of the FDP-TPR curves for simulated datasets based on NB GLMMs for each of 12 DE methods with θ = 2. (D) Line plot of the FDP-TPR curves for simulated datasets based on Poisson GLMMs for each of 12 DE methods with ${\mathrm{\beta }}_0={\mathrm{\sigma }}_{\mathrm{\beta }}^2=$ 0.01. Circles represent values at a 0.05 nominal FDR threshold and are filled in if the FDP (i.e., empirical FDR) is less than 0.05. DE, differential expression; GLMM, generalized linear mixed model; NB, negative binomial; TPR, true positive rate; FDP, false discovery proportion; FDR, false discovery rate.