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With calibrated scores, Käll’s method gives more discoveries than TDC. The ratio of the number of Käll discoveries to TDC discoveries at FDR ≤ 0.1 when using the calibrated score. The median ratio (with respect to 1000 independently drawn decoys) in solid line is flanked by the 0.95 and 0.05 quantiles of the ratios. After calibrating, all three scores typically yield more Käll than TDC discoveries at any given FDR.
