Table 2. Reliability of Quantifications for Detected Spots.
Summary of %CV for spots detected by various preprocessing methods, across all dilution series and treatment groups for differential expression studies. Methods include (1) Pinnacle, (2) SameSpots, (3) SameSpots with PG spot detection (SameSpots+PG), (4) SameSpots with manual editing with SameSpots (SameSpots+edits), (5) SameSpots with manual editing with PG (SameSpots+edits (PG)), (6) Progenesis PG240 (PG240).
| Study | Method | Number of Spots | %CV (Reliability) | |||||
|---|---|---|---|---|---|---|---|---|
| Mean | Q05 | Q25 | Median | Q75 | Q95 | |||
| NC | Pinnacle | 937 | 18.8 | 7.4 | 12.5 | 17.1 | 22.8 | 33.9 |
| SameSpots | 688 | 20.2 | 8.2 | 13.4 | 17.9 | 22.8 | 36.2 | |
| SameSpots +PG | 1033 | 22.7 | 8.0 | 13.7 | 18.5 | 24.4 | 44.4 | |
| SameSpots +edits | 900 | 20.2 | 7.9 | 13.4 | 17.9 | 23.0 | 35.7 | |
| SameSpots +edits (PG) | 1082 | 20.9 | 7.8 | 13.7 | 18.3 | 23.9 | 38.1 | |
| PG240 | 566 | 49.7 | 10.5 | 18.6 | 27.4 | 61.5 | 200.0 | |
| SH | Pinnacle | 1322 | 27.5 | 5.2 | 13.7 | 23.2 | 38.3 | 61.0 |
| SameSpots | 1037 | 29.9 | 5.9 | 15.5 | 26.4 | 41.1 | 64.4 | |
| SameSpots +PG | 1305 | 30.4 | 6.3 | 16.2 | 27.1 | 41.8 | 64.9 | |
| SameSpots +edits | 1244 | 29.4 | 5.7 | 15.4 | 25.6 | 40.5 | 64.0 | |
| SameSpots +edits (PG) | 1383 | 30.0 | 6.1 | 15.9 | 26.3 | 41.2 | 65.1 | |
| PG240 | 391 | 66.9 | 11.1 | 28.4 | 53.0 | 92.3 | 173.2 | |
| D1 | Pinnacle | 719 | 25.6 | 11.0 | 16.5 | 22.4 | 30.1 | 53.0 |
| SameSpots | 1094 | 43.8 | 22.5 | 30.7 | 37.8 | 51.6 | 85.6 | |
| SameSpots +PG | 1319 | 44.0 | 23.6 | 31.5 | 38.3 | 51.1 | 79.2 | |
| SameSpots +edits | 1153 | 40.5 | 22.5 | 31.0 | 36.8 | 46.6 | 69.3 | |
| SameSpots +edits (PG) | 1255 | 40.3 | 22.5 | 31.0 | 36.8 | 46.5 | 68.5 | |
| D2 | Pinnacle | 1136 | 28.8 | 10.4 | 16.2 | 21.9 | 31.4 | 75.0 |
| SameSpots | 1410 | 36.8 | 14.7 | 21.6 | 29.1 | 44.3 | 86.0 | |
| SameSpots +PG | 1928 | 36.7 | 15.3 | 23.4 | 32.2 | 44.7 | 72.0 | |
| SameSpots +edits | 1390 | 30.2 | 14.3 | 20.7 | 27.2 | 35.7 | 56.0 | |
| SameSpots +edits (PG) | 1458 | 30.3 | 14.2 | 20.8 | 27.5 | 36.1 | 55.6 | |