Fig. 2

Overall performance of the evaluated methods. The three circles for each method indicate the observed false discovery rate (FDR) and true positive rate (TPR) when the gene-wise q values are thresholded at three commonly used thresholds: 0.01, 0.05, and 0.1. Ideally, each circle should fall to the left of the corresponding vertical line, since this would indicate that the FDR is controlled at the imposed level. A circle is filled if the FDR is controlled and open otherwise. The total number of genes (n) and the number affected by differential isoform usage (n.ds) are given in the panel headers. Overall, only cuffdiff manages to control the FDR, but at the cost of a reduction in power (TPR). The FDR control is worse in the human simulation than in the fruit fly simulation, potentially due to the larger number of isoforms in the human transcriptome