Table 4.
Gene frequency occurrence for each simulated dataset and selection method.
| N | q | Training fraction | Occurrence frequency med (min–max) TP/FP |
|||||
|---|---|---|---|---|---|---|---|---|
| LASSO-cvl | LASSO-pcvl | Elastic Net | BSS Enet | CoxBoost | RSF | |||
| 500 | 0 | 1/2 | NA/1 (1-16) | NA/1 (1-19) | NA/1 (1-18) | NA/1 (1-26) | NA/1 (1-23) | NA/5 (1-71) |
| 2/3 | NA/1 (1-18) | NA/1 (1-21) | NA/1 (1-22) | NA/2 (1-40) | NA/1 (1-23) | NA/4 (1-94) | ||
| 12 | 1/2 | 76 (3-100)/2 (1-30) | 65 (2-100)/1 (1-13) | 86 (19-100)/2 (1-37) | 82 (19-100)/2 (1-28) | 74 (1-100)/2 (1-31) | 48 (9-94)/4 (1-89) | |
| 2/3 | 92 (8-100)/2 (1-50) | 86 (3-100)/2 (1-29) | 97 (34-100)/2 (1-64) | 97 (38-100)/2 (1-54) | 92 (10-100)/2 (1-59) | 52 (12-87)/4 (1-98) | ||
| 50 | 1/2 | 66 (1-99)/2 (1-53) | 58 (1-100)/2 (1-37) | 79 (1-100)/2 (1-67) | 68 (3-100)/2 (1-34) | 67 (1-99)/2 (1-46) | 18 (1-87)/4 (1-62) | |
| 2/3 | 89 (1-100)/2 (1-74) | 82 (6-100)/2 (1-57) | 94 (4-100)/3 (1-77) | 91 (1-100)/2 (1-64) | 87 (1-100)/2 (1-68) | 22 (1-100)/3 (1-81) | ||
|
| ||||||||
| 750 | 0 | 1/2 | NA/1 (1-14) | NA/1 (1-16) | NA/1 (1-17) | NA/1 (1-42) | NA/1 (1-10) | NA/3 (1-60) |
| 2/3 | NA/1 (1-13) | NA/1 (1-18) | NA/1 (1-14) | NA/2 (1-71) | NA/1 (1-14) | NA/2 (1-86) | ||
| 12 | 1/2 | 94 (22-100)/2 (1-34) | 90 (17-100)/1 (1-13) | 99 (39-100)/2 (1-38) | 98 (31-100)/1 (1-30) | 94 (22-100)/2 (1-34) | 59 (9-100)/3 (1-77) | |
| 2/3 | 99 (17-100)/2 (1-44) | 98 (12-100)/1 (1-15) | 100 (35-100)/2 (1-48) | 100 (28-100)/2 (1-42) | 99 (14-100)/2 (1-47) | 74 (11-100)/2 (1-60) | ||
| 50 | 1/2 | 78 (10-100)/2 (1-44) | 72 (6-100)/1 (1-31) | 90 (14-100)/2 (1-54) | 84 (6-100)/2 (1-31) | 76 (7-100)/2 (1-40) | 21 (1-86)/3 (1-56) | |
| 2/3 | 94 (13-100)/2 (1-68) | 91 (4-100)/2 (1-48) | 98 (28-100)/3 (1-78) | 97 (12-100)/2 (1-57) | 94 (11-100)/2 (1-56) | 35 (1-100)/2 (1-55) | ||
|
| ||||||||
| 1000 | 0 | 1/2 | NA/1 (1-20) | NA/1 (1-21) | NA/1 (1-22) | NA/2 (1-50) | NA/1 (1-26) | NA/2 (1-78) |
| 2/3 | NA/1 (1-39) | NA/1 (1-43) | NA/1 (1-40) | NA/2 (1-80) | NA/1 (1-40) | NA/2 (1-80) | ||
| 12 | 1/2 | 97 (5-100)/2 (1-53) | 97 (2-100)/1 (1-33) | 100 (15-100)/2 (1-64) | 99 (19-100)/2 (1-56) | 98 (5-100)/2 (1-57) | 70 (26-99)/2 (1-32) | |
| 2/3 | 100 (6-100)/2 (1-84) | 100 (2-100)/2 (1-49) | 100 (16-100)/3 (1-87) | 100 (21-100)/3 (1-89) | 100 (5-100)/2 (1-88) | 54 (28-100)/1 (1-14) | ||
| 50 | 1/2 | 98 (2-100)/2 (1-74) | 93 (11-100)/1 (1-48) | 99 (5-100)/3 (1-81) | 99 (20-100)/2 (1-64) | 95 (1-100)/2 (1-60) | 30 (1-95)/2 (1-48) | |
| 2/3 | 100 (2-100)/3 (1-93) | 100 (6-100)/2 (1-77) | 100 (5-100)/3 (1-97) | 100 (2-100)/2 (1-92) | 100 (7-100)/2 (1-86) | 36 (1-86)/2 (1-22) | ||