Figure 9

Estimation of the number of differentially expressed (DE) genes from simulated data. Boxplots of ratios of estimated to true numbers of DE genes obtained from data simulated from a hierarchical gamma-Poisson model with constant (a) and variable (b) library factors. This figure summarizes the results in Additional file 2: Figures S9 and S10 reporting estimated numbers of DE genes under different simulated scenarios of number or true DE genes and fold-change. The horizontal dash line at ratio one corresponds to the best performance where the estimated number of DE genes matches the true number.