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%) padj ≤ 0.01. B: FPR (Eq. 5 at α = 1%) padj ≤ 0.01. The solid grey line (“multiplex line”) connecting the TPR values of n biological replicates at <a onClick="popup('http://www.biomedcentral.com/1471-2164/13/484/mathml/M2','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/13/484/mathml/M2">View MathML</a> 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.

Robles et al. BMC Genomics 2012 13:484   doi:10.1186/1471-2164-13-484
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