Table 6.
Effect of Applying Standard Thresholds (Compared to Optimized Thresholds) to Diploid, Triploid, and Hypertriploid Samples
| Ploidy | Diploid | Triploid | Hypertriploid |
|---|---|---|---|
| Gain threshold applied | 1.18 | ||
| [log2 ratio value] | [0.24] | ||
| Sensitivity | 0.85 | 0.74 | 0.21 |
| (% change) | (−6.6) | (−13) | (−70) |
| Specificity | 0.94 | 0.96 | 0.96 |
| (% change) | (+3.3) | (+13) | (+35) |
| Probability of error | 0.21 | 0.30 | 0.83 |
| (% change) | (+17) | (0) | (+43) |
| Loss threshold applied | 0.85 | ||
| [log2 ratio value] | [−0.24] | ||
| Sensitivity | 0.99 | 0.90 | 0.38 |
| (% change) | (+2.1) | (−2.2) | (−49) |
| Specificity | 0.95 | 0.93 | 0.95 |
| (% change) | (−2.1) | (+1.1) | (+28) |
| Probability of error | 0.060 | 0.17 | 0.67 |
| (% change) | (0) | (+6.3) | (+29) |
Standard thresholds are at ±3 SDs of the mean of normal-normal hybridizations. Numbers in brackets indicate percent change from the optimized rates obtained using ploidy-specific thresholds.