Table 1.
Median proportions of missing values and interquartile range (IQR) mean proportions of missing valid result scores in the semi-simulated spike-in datasets and the experimental Francisella tularensis subspecies novicida dataset
| UPS1 Filtered | SGSDS Filtered | UPS1Mix Filtered | UPS1 Full | SGSDS Full | CPTAC Full | UPS1Mix Full | WT vs. L | WT vs. D2 | WT vs. D1 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Missing values in proteins | ||||||||||
| All proteins | 0.0% | 0.0% | 0.0% | 14.1% | 3.3% | 19.6% | 14.0% | 7.0% | 7.7% | 7.1% |
| Spike-in proteins | 0.0% | 0.0% | 0.0% | 0.0% | 4.6% | 28.5% | 0.0% | |||
| Missing values in results | ||||||||||
| BaselineROTS | 0.0% | 0.0% | 0.0% | 11.0% | 1.8% | 15.2% | 9.0% | 2.0% | 1.8% | 2.3% |
| Lme | 0.0% | 0.0% | 0.0% | 7.7% | 0.5% | 7.4% | 7.2% | 1.5% | 1.4% | 1.3% |
| Pme_H | 0.0% | 0.0% | 0.0% | 19.3% | 3.2% | 19.5% | 19.1% | 13.2% | 16.1% | 12.7% |
| Pme_L | 0.0% | 0.0% | 0.0% | 11.9% | 1.2% | 11.4% | 11.2% | 2.8% | 2.7% | 2.7% |
| LMMS | 0.0% | 0.0% | 0.0% | 4.8% | 0.6% | 5.9% | 4.0% | 0.8% | 0.7% | 0.8% |
| MaSigPro_H | 20.3% | 22.8% | 23.2% | 30.6% | 24.1% | 40.6% | 32.9% | 29.3% | 31.4% | 16.7% |
| MaSigPro_L | 33.6% | 35.7% | 46.0% | 41.1% | 36.5% | 52.2% | 51.8% | 43.6% | 51.2% | 26.8% |
| BETR | 0.0% | 0.0% | 0.0% | NA | NA | NA | NA | 29.6% | 34.1% | 32.2% |
| Timecourse | 0.0% | 0.0% | 0.0% | 23.4% | 6.9% | 27.8% | 24.4% | 20.8% | 25.0% | 23.5% |
| Limma | 0.0% | 0.0% | 0.0% | 19.3% | 3.2% | 19.2% | 19.0% | 13.2% | 16.1% | 12.7% |
| LimmaSplines_H | 0.0% | 0.0% | 0.0% | 19.3% | 3.2% | 19.2% | 19.0% | 13.2% | 16.1% | 12.7% |
| LimmaSplines_L | 0.0% | 0.0% | 0.0% | 11.9% | 1.2% | 11.1% | 11.1% | 2.7% | 2.7% | 2.6% |
| EDGE_H | 0.0% | 0.0% | 0.0% | 34.2% | 15.0% | 50.7% | 33.8% | 29.6% | 34.1% | 32.2% |
| EDGE_L | 0.0% | 0.0% | 0.0% | 34.3% | 15.0% | 50.7% | 33.8% | 29.6% | 34.1% | 32.2% |
| OmicsLonDA | 0.0% | 0.0% | 0.0% | 21.8% | 4.3% | 25.6% | 21.6% | 11.6% | 16.2% | 13.4% |
| RolDE | 0.0% | 0.0% | 0.0% | 0.0% | 0.0% | 0.0% | 0.0% | 0.0% | 0.0% | 0.0% |
NA refers to no scores delivered at all by the method. Source data are provided as a Source Data file.