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Figure 3 | BMC Genomics

Figure 3

From: Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing

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 1 n ×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.

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