Table 3. Empirical evaluation of the performance of the COMBI method on the WTCCC data, relative to that of basic RPVT.
| Number of SNPs reaching significance applying |
||
|---|---|---|
| RPVT | COMBI Method | |
| SNPs that have achieved <10−5 in at least one external study | 24 (32% precision) | 28 (61% precision) |
| SNPs that have not achieved <10−5 in an external study | 52 (68% error) | 18 (39% error) |
| Overall | 76 | 46 |
| p-value (one-sided Fisher’s exact test) | 0.0014 | |
The table represents the information given by the points on the RPVT and COMBI lines in Fig. 4. The final results of the two methods when applying the corresponding significance thresholds are shown. At significance threshold t* = 10−5, COMBI achieves 28 SNPs recall at precision 61%, while RPVT achieves a recall of only 24 SNPs at precision 32%.