(A). Original MDR analysis of unbalanced data. | |||
---|---|---|---|
Number of loci in model | Best candidate model | Average cross-validation consistency | Average prediction error |
1 | 1 | 10 | 20.00% |
2 | 7, 8 | 7 | 21.28% |
3 | 3, 5, 10 | 5 | 22.90% |
4 | 2, 3, 5, 10 | 4 | 26.60% |
5 | 1, 4, 7, 8, 9 | 4 | 29.66% |
Final model: locus 1 -- INCORRECT MODEL | |||
(B). Alnalysis using threshold adjustment only. | |||
Number of loci in model | Best candidate model | Average cross-validation consistency | Average prediction error |
1 | 5 | 5 | 40.80% |
2 | 4, 9 | 3 | 30.53% |
3 | 4, 5, 7 | 7 | 31.74% |
4 | 3, 5, 8, 10 | 4 | 36.60% |
5 | 1, 2, 4, 5, 9 | 5 | 40.00% |
Final model: loci 4 and 9 -- INCORRECT MODEL | |||
(C). Analysis using threshold adjustment and balanced accuracy. | |||
Number of loci in model | Best candidate model | Average cross-validation consistency | Average prediction error |
1 | 8 | 6 | 49.50% |
2 | 10, 5 | 4 | 45.75% |
3 | 10, 5, 3 | 10 | 29.97% |
4 | 10, 5, 3, 2 | 7 | 33.69% |
5 | 10, 8, 5, 4, 3 | 6 | 41.86% |
Final model: loci 3, 5, 10 -- CORRECT MODEL | |||
(D). Analysis of over-sampled data. | |||
Number of loci in model | Best candidate model | Average cross-validation consistency | Average prediction error |
1 | 8 | 9 | 46.25% |
2 | 5, 10 | 3 | 46.75% |
3 | 3, 5, 10 | 10 | 25.84% |
4 | 3, 5, 8, 10 | 7 | 29.83% |
5 | 3, 5, 6, 8, 10 | 5 | 25.88% |
Final model: loci 3, 5, 10 -- CORRECT MODEL | |||
(E). Analysis of under-sampled data. | |||
Number of loci in model | Best candidate model | Average cross-validation consistency | Average prediction error |
1 | 6 | 5 | 60.00% |
2 | 5, 10 | 10 | 32.56% |
3 | 3, 5, 10 | 10 | 28.00% |
4 | 3, 5, 7, 10 | 7 | 32.53% |
5 | 3, 4, 5, 6, 10 | 4 | 39.95% |
Final model: loci 3, 5, 10 -- CORRECT MODEL | |||
(F). Analysis using misclassification error for model selection. | |||
Number of loci in model | Best candidate model | Average classification error | |
1 | 1 | 20.00% | |
2 | 7, 8 | 18.79% | |
3 | 3, 5, 10 | 18.00% | |
4 | 2, 3, 5, 10 | 16.80% | |
5 | 1, 4, 7, 8, 9 | 15.60% | |
Final model: loci 1, 4, 7, 8, 9 -- INCORRECT MODEL |