Fig. 5

FDP-TPR performance curves for DTE analysis of the simulated data. Blue curves represent transcript-level tests, and green curves represent tests based on p values aggregated at the gene level. The orange curve represents the stage-wise transcript-level analysis. The three open circles on the curves represent working points for a target FDR of 1%, 5% and 10%. a Performance curve for the Drosophila simulation shows an inflated FDR for both the aggregated analysis on the gene level and a transcript-level analysis. The stage-wise transcript-level analysis has increased performance and additionally provides a better FDR control. b Performance curve for the human simulation shows even worse FDR control on all levels, which is in line with previous publications [24]. Similar to the Drosophila simulation, the transcript-level stage-wise analysis shows somewhat higher performance and provides a better FDR control