Table 2.
Contrasting Birdseedv2 results in Table 1 using 32,752 non-missing consensus HapMap calls
| Original | Spatial normalization | ||
|---|---|---|---|
| Agree | Disagree | Missing | |
| Agree | - | 1,176 (3.6) |
7,690 (23.5) |
| Disagree | 2,518 (7.7) |
7 (0.02) |
2,716 (8.3) |
| Missing | 16,887 (51.6) |
1,758 (5.4) |
0 |
Entries are frequencies (percentages) out of the 32,752 genotypes. Agreement and disagreement are with respect to the non-missing consensus HapMap calls. Separate one tailed McNemar's tests on the three pairs of discordant entries suggest significant improvement in favor of the use of spatial normalization: i.) z = 22.1 for agree versus disagree; ii.) z = 58.7 for agree versus missing; and iii.) z = 14.3 for disagree versus missing.