TABLE 1.
Comparison of results before and after the removal of SNP-containing probes
| snp-free-ps (snp-ps)
|
||||
|---|---|---|---|---|
| Tests | Significance level (FDR) | Before | After | Common |
| F-test for samples | 0.001 | 5601 (542) | 5623 (509) | 5599 (460) |
| Mouse effect | 0.05 | 1618 (136) | 1526 (128) | 1526 (114) |
| Strain effect | 0.05 | 8186 (793) | 7855 (766) | 7854 (648) |
| A vs. B | 0.05 | 8149 (801) | 7655 (792) | 7655 (672) |
| F1(A × B) vs. F1(B × A) | 0.05 | 292 (22) | 217 (16) | 217 (9) |
| F1's vs. parents | 0.05 | 60 (7) | 60 (5) | 60 (4) |
| AB dominance | 0.05 | 295 (22) | 525 (46) | 295 (18) |
| BA dominance | 0.05 | 19 (4) | 19 (2) | 19 (2) |
| AB overdominance | 0.05 | 149 (9) | 122 (9) | 122 (4) |
| BA overdominance | 0.05 | 18 (0) | 17 (1) | 17 (0) |
Eight snp-ps probe sets were removed from testing because there were fewer than four probes remaining. Snp-free-ps, significant probe sets that do not contain any known SNP in any probes; snp-ps, significant probe sets that contain an SNP in one or more probes.