Effect of iterations for an RDR6 knockout dataset. (a) AUC values for four XXX-edgeR combinations with different iteration numbers (n = 0 ~ 30) when using a default floor PDEG value (= 5%) are shown: XXX = iDEGES/TbT (red lines), iDEGES/edgeR (black lines) , iDEGES/TDT (blue lines) , and iDEGES/DESeq (light blue lines). The AUC values after convergence were 69.64% for iDEGES/TbT at the 3rd iteration and 64.88% for iDEGES/DESeq at the 2nd iteration. The maximum and minimum values among cycles for iDEGES/edgeR were 67.37% and 64.57%, respectively. Note that the AUC values for three pipelines (iDEGES/TbT, iDEGES/edgeR, and iDEGES/TDT) are the same (= 68.36%) when n = 0 because those pipelines correspond to XXX = TMM (i.e., the TMM-edgeR combination). The first cycle for the non-convergent (P) results is indicated by a brace. (b) AUC values when using a 10% floor PDEG value are shown. The NP values for iDEGES/TbT, iDEGES/edgeR, and iDEGES/TDT were 8, 3, and 3, respectively.