Figure 3

TPR and FPR detected by DESeq as a function of sequencing depth and replication. Different symbols represent the number n of control vs. treatment samples (n = 2, 3, 4, 6, 8, and 12) across sequence depths [100%→1%]. A: TPR (Eq. 6 at α = 1%) p_adj ≤ 0.01. B: FPR (Eq. 5 at α = 1%) p_adj ≤ 0.01. The solid grey line (“multiplex line”) connecting the TPR values of n biological replicates at$\frac{1}{n}\times 100\%$ sequencing depth shows the increase of TPR as more biological replicates n are used despite the loss power due to the sequencing depth reduction required by the multiplexing of lanes. This trend remains true even for the n = 32 and n = 96 cases.