Table 2.
Evaluate the Performance of the Multigene Signature by Four Algorithms Averaged Across 10-Fold CVs in the METABRIC Cohort
| Measures | EMP | NB | Logistic | optAUC |
|---|---|---|---|---|
| Specificity | 0.99 | 0.97 | 0.99 | 0.96 |
| Sensitivity | 0.71 | 0.94 | 0.79 | 0.96 |
| NPV | 0.97 | 0.99 | 0.98 | 1.00 |
| PPV | 0.91 | 0.74 | 0.88 | 0.71 |
| Accuracy | 0.97 | 0.97 | 0.97 | 0.96 |
| Youden | 0.70 | 0.91 | 0.78 | 0.92 |
| Youden* | 0.71 | 0.94 | 0.79 | 0.96 |
| FP/TP | 0.11 | 0.40 | 0.16 | 0.44 |
| FN/TN | 0.03 | 0.01 | 0.02 | 0.00 |
As evaluated against FGFR1 amplification by diagnostic measures, all algorithms perform well; optAUC led to the lowest FN/TN and the highest sensitivity and NPV.
CV, cross-validation; EMP, empirical method; FN, false negative; FP, false positive; Logistic, logistic regression; METABRIC, Molecular Taxonomy of Breast Cancer International Consortium; NB, naïve Bayes method; NPV, negative predictive value; optAUC, optimal area under the receiver operating characteristic curve; PPV, positive predictive value; TN, true negative, TP, true positive; Youden, does not consider population prevalence and uses equal weight on sensitivity and specificity; Youden*, considers population prevalence and allows different penalty/cost on FP and FN.