Figure 3.

Impact of unequal sample sizes. Pairwise comparisons of perfect in silico replicate RNA-Seq datasets were made similarly to Figure 2, but keeping the total read count for each pair constant while systematically varying the relative size of both datasets, e.g., 1x10⁶ plus 9x10⁶, 3 x10⁶ plus 7 x10⁶, 5 x10⁶ plus 5 x10⁶. Pearson’s r and Kappa fell for unequal sample sizes demonstrating a maximum for equal sample sizes. SERE remained stable at 1.0 while the 99% CI of repeat measures was optimal (smallest) for equal sample sizes.