* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * EVALUATING STATISTICAL SIGNIFICANCE * * * * IN TWO-STAGE GENOMEWIDE ASSOCIATION STUDIES * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Test Data Created From the HapMap Data DATA FILE: test.dat OUTPUT FILE: test.out TOTAL SAMPLE SIZE = 2000 TOTAL NUMBER OF MARKERS = 1393 SAMPLE SIZE IN STAGE 1 = 1000 CRITICAL VALUE FOR STAGE 1 = 3.00000 NUMBER OF MONTE CARLO SAMPLES = 10000 UNADJUSTED ADJUSTED P-VALUES MARKER TEST STAT P-VALUE HOLM LIN ------ --------- ------------ ---------- ---------- 1129 18.334 0.0000185417 0.02582855 0.00830000 1124 18.316 0.0000187173 0.02605445 0.00850000 1165 17.725 0.0000255291 0.03551095 0.01190000 1116 17.600 0.0000272569 0.03788713 0.01250000 1099 17.469 0.0000292071 0.04056861 0.01330000 1096 17.332 0.0000313776 0.04355209 0.01420000 1142 17.304 0.0000318463 0.04417075 0.01430000 1121 16.943 0.0000385092 0.05337378 0.01740000 1149 16.783 0.0000419180 0.05805648 0.01890000 1084 16.027 0.0000624389 0.08641542 0.02540000 1077 15.938 0.0000654650 0.09053804 0.02620000 1118 15.741 0.0000726494 0.10040149 0.03040000 1100 15.739 0.0000727276 0.10043680 0.03050000 1085 15.508 0.0000821497 0.11336659 0.03380000 1109 15.416 0.0000862757 0.11897414 0.03490000 1333 14.911 0.0001127097 0.15531402 0.04430000 1074 14.148 0.0001690077 0.23272354 0.06230000 1071 14.055 0.0001775006 0.24424089 0.06490000 1305 13.568 0.0002300836 0.31636496 0.08220000 1182 12.946 0.0003206117 0.44052050 0.10870000 1179 12.732 0.0003595280 0.49363188 0.11870000 1261 12.618 0.0003820378 0.52415582 0.12390000 1185 12.229 0.0004705374 0.64510678 0.14660000 1062 11.899 0.0005616752 0.76949498 0.16860000 1378 11.496 0.0006973340 0.95465025 0.20040000 1338 11.117 0.0008553612 1.00000000 0.23620000 1113 10.894 0.0009648160 1.00000000 0.25710000 1183 10.770 0.0010313605 1.00000000 0.26890000 1044 10.465 0.0012168289 1.00000000 0.30180000 107 9.419 0.0021469781 1.00000000 0.43100000 1064 9.255 0.0023486852 1.00000000 0.45100000 1164 8.994 0.0027088873 1.00000000 0.48690000