Figure 11.

Semicalibrated scores mostly yield more discoveries than using raw scores (TDC, FDR levels > 2%). Each panel plots, as a function of FDR threshold, the ratio of the number of TDC discoveries at a given FDR threshold when using the semicalibrated score (numerator) versus the number of discoveries at the same FDR when using the raw score (denominator). The solid line represents the median ratio with respect to 1000 independently drawn decoy sets, whereas the 0.95 and 0.05 quantiles of the ratios are represented as dots.