Table 2.
Results achieved with the three methods for estimating variant FDRs on simulated data, with the FDR control level at 1%
| n | iCombined FDR | iSeparate FDR | iTransfer FDR | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Ave.#I.D.s | Est.error(%) | Ave.#I.D.s | Est.error(%) | Ave.#I.D.s | Est.error(%) | ||||
| (false/all) | Mean | SD | (false/all) | Mean | SD | (false/all) | Mean | SD | |
| 1 | 10.22/10.70 | -94.36 | 5.13 | 0.21/0.55 | -16.95 | 34.64 | 0.00/0.25 | 0.00 | 0.02 |
| 5 | 10.76/13.09 | -80.95 | 8.84 | 0.30/2.05 | -11.09 | 20.57 | 0.00/1.24 | 0.01 | 0.07 |
| 10 | 10.09/14.87 | -66.43 | 9.50 | 0.60/4.17 | -12.92 | 11.63 | 0.00/2.50 | 0.04 | 0.14 |
| 20 | 10.90/20.57 | -51.64 | 9.08 | 0.72/ 8.07 | -8.86 | 6.31 | 0.00/5.30 | 0.08 | 0.19 |
| 50 | 10.53/34.44 | -29.25 | 6.87 | 0.73/19.07 | -3.60 | 2.57 | 0.00/13.28 | 0.20 | 0.27 |
| 100 | 10.67/58.64 | -17.09 | 4.54 | 0.73/38.27 | -1.43 | 1.25 | 0.00/27.40 | 0.42 | 0.35 |
Note: n, the number of variant mass spectra; Ave.#I.D.s, average number of false/all identifications of variant peptides from the target database at 1% estimated FDR; Est.error, the difference between the estimated FDR and the real FDR; Mean and SD, mean and standard deviation of the Est.error as percentage