Table 3. Differential Expression Comparison, Comparative Proteomics Studies.
Summary of performance of preprocessing methods in detecting differential expression in comparative proteomics studies. The p-values are from two-sample t-tests performed on the log-transformed spot quantifications for the various methods. The q-values are local FDR estimates, and measure the probability that a given spot would be a false positive if it is declared differentially expressed.
| Method | Number of Spots | q-values | p-values | |||||
|---|---|---|---|---|---|---|---|---|
| <0.15 | <0.20 | <0.001 | <0.005 | <0.01 | <0.05 | |||
| D1 | Pinnacle | 719 | 2 | 3 | 3 | 6 | 17 | 76 |
| SameSpots | 1094 | 0 | 0 | 0 | 0 | 1 | 17 | |
| SameSpots +PG | 1319 | 0 | 0 | 0 | 1 | 3 | 24 | |
| SameSpots +edits | 1153 | 0 | 0 | 0 | 0 | 1 | 11 | |
| SamesSpots +edits (PG) | 1255 | 0 | 0 | 0 | 0 | 1 | 13 | |
| D2 | Pinnacle | 1136 | 5 | 7 | 5 | 10 | 20 | 107 |
| SameSpots | 1410 | 0 | 0 | 2 | 11 | 24 | 123 | |
| SameSpots +PG | 1928 | 0 | 0 | 2 | 16 | 35 | 151 | |
| SameSpots +edits | 1390 | 0 | 0 | 1 | 14 | 32 | 157 | |
| SamesSpots +edits (PG) | 1458 | 0 | 0 | 0 | 12 | 27 | 159 | |