Table 1 Performance comparison of analysis order-based normalization methods using QC runs and the number of statistically significant ions between cases and controls
From: Gaussian process regression model for normalization of LC-MS data using scan-level information
Batch | Raw | LOESS | LOESS-CV | GPRM | GPRM-EIC | 2D-GPRM-EIC |
|---|---|---|---|---|---|---|
1 Positive | 5.0 | 5.2 | 4.6 | 2.9 | 2.5 | 2.1 |
2 Positive | 7.0 | 4.3 | 3.7 | 2.5 | 2.2 | 1.8 |
1 Negative | 5.0 | 3.8 | 3.6 | 3.0 | 2.6 | 2.2 |
2 Negative | 20 | 12 | 10.9 | 6.8 | 5.7 | 4.4 |
(A) Percentage of the number of ions with significant QC variation (q ζ < 0.1) | ||||||
Mode | Raw | LOESS | LOESS-CV | GPRM | GPRM-EIC | 2D-GPRM-EIC |
Positive | 23 | 27 | 30 | 37 | 39 | 42 |
Negative | 11 | 19 | 21 | 28 | 31 | 33 |
(B) Number of statistically significant ions between cases and controls, overlapping in batch B1 and B2 | ||||||