Table 2.
Comparison of the mean difference in relative standard deviation across quality control samples between normalization approaches using paired t-tests.1
| Compared Normalization Approaches | RPLC Data | HILIC Data | ||
|---|---|---|---|---|
| RSD Mean Difference 3 | p-value | RSD Mean Difference 3 | p-value | |
| Raw and SVR 2 | 0.100 | p < 2.2 × 10−16 | 0.160 | p < 2.2 × 10−16 |
| SVR and Creatinine 2,4 | −0.040 | p < 2.2 × 10−16 | −0.002 | 0.21 |
| SVR and Specific Gravity 2,4 | 0 | -- | 0 | -- |
| SVR and PQN 2 | 0.075 | p < 2.2 × 10−16 | 0.100 | p < 2.2 × 10−16 |
| Creatinine and Specific Gravity 2,4 | 0.040 | p < 2.2 × 10−16 | 0.002 | 0.21 |
| Creatinine and PQN 2 | 0.116 | p < 2.2 × 10−16 | 0.103 | p < 2.2 × 10−16 |
| Specific gravity and PQN 2 | 0.075 | p < 2.2 × 10−16 | 0.101 | p < 2.2 × 10−16 |
1 Abbreviations: RPLC, reversed-phase liquid chromatography; HILIC, hydrophilic interaction chromatography; RSD, relative standard deviation; SVR, support vector regression; PQN, probabilistic quotient normalization; SGref, reference specific gravity; SG, specific gravity; QC, quality control sample. 2 Raw data were processed using XCMS. SVR normalization was then applied to all datasets. Creatinine, specific gravity, and PQN adjustments were carried out after SVR normalization. 3 RSD mean differences are computed in the order listed, for example, RSDraw–RSDSVR, and expressed as percentages. 4 Because of the specific gravity normalization method in which SGref = SG for QC samples (see Section 4.6, Equation (1)), QC peak areas are the same as those normalized by SVR alone, and therefore there is no difference in the RSD when comparing these methods. Similarly, because QC peak areas are the same for specific gravity and SVR, comparisons between creatinine and SVR and creatinine and specific gravity result in the same mean differences in terms of absolute value, and the same p-values.