Table 2.
The P-values in paired t-tests of differences for power and mean absolute deviation (MAD) between the new (GCIM-random and GCIM-fixed) and current (ICIM and CIM) methods
| QTL | GCIM-random (A) and GCIM- fixed (B) |
GCIM-random (A) and ICIM (B) |
GCIM-random (A) and CIM (B) |
GCIM-fixed (A) and ICIM (B) |
GCIM- fixed (A) and CIM (B) |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Power | MAD (Add) | MAD (Dom) | Power | MAD (Add) | MAD (Dom) | Power | MAD (Add) | MAD (Dom) | Power | MAD (Add) | MAD (Dom) | Power | MAD (Add) | MAD (Dom) | |
| The first simulation experiment (phenotype = mean + 19 main-effect QTLs + residual error with normal distribution) | |||||||||||||||
| All | 3e-04*** (5.711) | 0.9645 (−0.001) | 0.0000*** (0.033) | 1e-04*** (30.026) | 0.9046 (0.007) | 0.011* (−0.141) | 0.0000*** (43.447) | 0.0232 (−0.211) | 4e-04*** (−0.328) | 1e-04*** (24.316) | 0.9020 (0.008) | 0.0043** (−0.174) | 0.0000*** (37.737) | 0.0240* (−0.211) | 2e-04*** (−0.361) |
| Small | 0.0606 (6.833) | 0.0729 (0.016) | 0.0293* (0.063) | 0.0617 (17.167) | 0.1564 (−0.138) | 0.0047** (−0.258) | 0.0260* (26.833) | 0.0732 (−0.302) | 0.0026** (−0.452) | 0.080 (10.333) | 0.1302 (−0.154) | 0.0031** (−0.321) | 0.0473* (20.000) | 0.0671 (−0.318) | 0.0011** (−0.515) |
| Large | 1.0000 (0.000) | 0.2078 (0.018) | 0.2406 (0.023) | 1.0000 (0.000) | 0.7253 (0.168) | 0.4038 (0.200) | 0.3608 (2.750) | 0.7512 (0.161) | 0.4245 (0.271) | 1.0000 (0.000) | 0.7477 (0.150) | 0.4617 (0.176) | 0.3608 (2.750) | 0.7732 (0.143) | 0.4663 (0.247) |
| Linked | 0.0016** (6.286) | 0.6592 (−0.007) | 0.0014** (0.028) | 1e-04*** (37.071) | 0.8206 (0.015) | 0.0088** (−0.164) | 0.0000*** (52.821) | 0.0288 (−0.245) | 2e-04*** (−0.386) | 2e-04*** (30.786) | 0.759 (0.022) | 0.0053** (−0.192) | 1e-04*** (46.536) | 0.0348* (−0.238) | 1e-04*** (−0.414) |
| The second simulation experiment (phenotype = mean + 19 main-effect QTLs + polygenic background + residual error with normal distribution) | |||||||||||||||
| All | 0.0029** (5.211) | 2e-04*** (0.039) | 2e-04*** (0.059) | 0.0000*** (36.158) | 0.8896 (0.009) | 0.0289* (−0.122) | 0.0000*** (50.474) | 0.0415* (−0.242) | 4e-04*** (−0.345) | 0.0000*** (30.947) | 0.6424 (−0.03) | 0.0018** (−0.181) | 0.0000*** (45.263) | 0.0179* (−0.280) | 1e-04*** (−0.404) |
| Small | 0.0397* (11.500) | 0.0394* (0.054) | 0.0517 (0.092) | 0.0788 (28.833) | 0.1865 (−0.156) | 0.0098** (−0.220) | 0.0469* (35.000) | 0.1055 (−0.363) | 0.0049** (−0.430) | 0.1382 (17.333) | 0.1405 (−0.211) | 8e-04*** (−0.312) | 0.0717 (23.500) | 0.0908 (−0.417) | 0.0085** (−0.522) |
| Large | 0.5000 (−0.250) | 0.3454 (0.060) | 0.3431 (0.150) | 0.5000 (1.250) | 0.7323 (0.187) | 0.0726 (0.325) | 0.5000 (0.250) | 0.8306 (0.140) | 0.1576 (0.421) | 0.5000 (1.500) | 0.7957 (0.127) | 0.4003 (0.175) | 0.5000 (0.500) | 0.8945 (0.080) | 0.3997 (0.270) |
| Linked | 0.0207* (4.643) | 0.0075** (0.032) | 3e-04*** (0.039) | 0.0000*** (42.714) | 0.7784 (0.018) | 0.0052** (−0.164) | 0.0000*** (60.964) | 0.0615 (−0.270) | 0.0000*** (−0.436) | 0.0000*** (38.071) | 0.8481 (−0.014) | 0.0018** (−0.203) | 0.0000*** (56.321) | 0.0367* (−0.303) | 0.0000*** (−0.475) |
| The third simulation experiment (phenotype = mean + 19 main-effect QTLs + residual error with log-normal distribution) | |||||||||||||||
| All | 0.0032** (3.789) | 0.7010 (−0.003) | 0.0082** (0.019) | 0.0000***(27.868) | 0.040** (−0.123) | 1e-04*** (−0.207) | 0.0000*** (43.947) | 0.0226* (−0.205) | 3e-04*** (−0.340) | 0.0000*** (24.079) | 0.0534 (−0.120) | 1e-04*** (−0.227) | 0.0000*** (40.158) | 0.0218* (−0.203) | 2e-04*** (−0.360) |
| Small | 0.1060 (6.167) | 0.1147 (0.015) | 0.0052** (0.024) | 0.0298* (17.000) | 0.0503 (−0.232) | 0.0075** (−0.329) | 0.0179* (24.667) | 0.084 (−0.231) | 0.0025** (−0.514) | 0.1296 (10.833) | 0.0524 (−0.247) | 0.0071** (−0.352) | 0.0743 (18.500) | 0.0826 (−0.246) | 0.0024** (−0.538) |
| Large | 0.5000 (−0.250) | 0.6107 (−0.010) | 0.4001 (−0.010) | 0.5000 (−0.250) | 0.9015 (0.042) | 0.8582 (0.061) | 1.0000 (0.000) | 0.7854 (0.121) | 0.4751 (0.262) | 1.0000 (0.000) | 0.8839 (0.053) | 0.8406 (0.071) | 0.5000 (0.250) | 0.7772 (0.131) | 0.4727 (0.271) |
| Linked | 0.0152* (3.857) | 0.5446 (−0.005) | 0.0176 (0.023) | 0.0000*** (34.214) | 0.0856 (−0.123) | 1e-04*** (−0.22) | 0.0000*** (54.357) | 0.0281* (−0.246) | 2e-04*** (−0.389) | 0.0000*** (30.357) | 0.1109 (−0.118) | 0.0000*** (−0.242) | 0.0000**** (50.5) | 0.0263* (−0.241) | 1e-04**** (−0.412) |
Note: *, ** and ***: significance at the 0.05, 0.01 and 0.001 levels, respectively.
Note: Small QTL: QTL1, QTL11 and QTL15; large QTL: QTL14 and QTL19; linked QTL: QTL2∼QTL10, QTL12∼QTL13 and QTL16∼QTL18. The differences (A−B) were in the brackets.