...
Comparing the Sage code base to the UCLA-based package, we see a difference in the selection of the 'soft threshold' (beta):
Sage power table / UCLA Package power table (The optimum chosen by each is highlighted)
...
Unequal beta, module diff=44% | identical beta, module diff=0.9% |
|---|---|
turquoise blue grey | turquoise blue grey |
Colon cancer, top 5K genes
Soft Threshold Choice
Cut | p-value | Adj R^2 | Truncated Adj R^2 | slope | mean(k) | median(k) | max(k) | Power | SFT.R.sq | slope | truncated.R.sq | mean.k. | median.k. | max.k. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | -1 | 0.0227 | 0.628 | 0.245 | 1120 | 1080 | 2090 | 1 | 0.076261431 | 0.197158442 | 0.578527312 | 1124.638974 | 1080.609612 | 2089.60932 |
1.5 | -1 | 0.303 | 0.63 | -0.361 | 664 | 583 | 1560 | 1.5 | 0.48169911 | -0.404715749 | 0.667548985 | 664.3731336 | 582.9224274 | 1556.715216 |
2 | -1 | 0.693 | 0.795 | -0.657 | 427 | 330 | 1220 | 2 | 0.804272633 | -0.671388746 | 0.848889263 | 426.8848938 | 329.8816149 | 1215.968849 |
2.5 | -1 | 0.794 | 0.851 | -0.821 | 292 | 195 | 988 | 2.5 | 0.83774129 | -0.824722962 | 0.860045069 | 291.5785624 | 194.5178802 | 987.8658261 |
3 | -1 | 0.803 | 0.858 | -0.921 | 209 | 121 | 822 | 3 | 0.835678099 | -0.929654091 | 0.857157416 | 208.5830425 | 120.747754 | 822.3388256 |
3.5 | -1 | 0.778 | 0.843 | -1.01 | 155 | 77.7 | 697 | 3.5 | 0.854303701 | -0.991173832 | 0.88464139 | 154.6909499 | 77.68335319 | 697.1742337 |
4 | -1 | 0.797 | 0.86 | -1.06 | 118 | 50.4 | 600 | 4 | 0.858882119 | -1.038499794 | 0.896861118 | 118.0810366 | 50.39027229 | 599.5206128 |
4.5 | -1 | 0.805 | 0.875 | -1.1 | 92.3 | 33.2 | 521 | 4.5 | 0.838656539 | -1.088724946 | 0.885484443 | 92.28466832 | 33.16210354 | 521.4428092 |
5 | -1 | 0.806 | 0.881 | -1.14 | 73.6 | 22.7 | 458 | 5 | 0.825292656 | -1.128907991 | 0.87822147 | 73.55040348 | 22.67682493 | 457.77922 |
5.5 | -1 | 0.796 | 0.881 | -1.17 | 59.6 | 15.6 | 405 | 5.5 | 0.83215391 | -1.150386899 | 0.897853335 | 59.59567098 | 15.64824143 | 405.0274823 |
6 | -1 | 0.804 | 0.895 | -1.2 | 49 | 11.1 | 361 | 6 | 0.845996532 | -1.170462192 | 0.912613381 | 48.974624 | 11.08447179 | 360.7272536 |
6.5 | -1 | 0.802 | 0.902 | -1.22 | 40.7 | 8.15 | 323 | 6.5 | 0.847401052 | -1.190785046 | 0.919920844 | 40.73957671 | 8.15415001 | 323.099656 |
7 | -1 | 0.82 | 0.916 | -1.23 | 34.3 | 6 | 291 | 7 | 0.852903615 | -1.206125559 | 0.930763629 | 34.25083811 | 6.002829394 | 290.8269204 |
7.5 | -1 | 0.824 | 0.925 | -1.25 | 29.1 | 4.56 | 263 | 7.5 | 0.853122377 | -1.223895553 | 0.937931424 | 29.06544208 | 4.562225559 | 262.9124211 |
8 | -1 | 0.828 | 0.933 | -1.26 | 24.9 | 3.46 | 239 | 8 | 0.852375009 | -1.242759963 | 0.940436732 | 24.8696934 | 3.456350492 | 238.5887885 |
8.5 | -1 | 0.837 | 0.943 | -1.28 | 21.4 | 2.68 | 217 | 8.5 | 0.864808 | -1.252939098 | 0.94865967 | 21.43698937 | 2.680344008 | 217.2558463 |
9 | -1 | 0.845 | 0.948 | -1.29 | 18.6 | 2.14 | 198 | 9 | 0.868297799 | -1.270639687 | 0.954031038 | 18.60071642 | 2.140872759 | 198.437645 |
9.5 | -1 | 0.844 | 0.948 | -1.31 | 16.2 | 1.79 | 182 | 9.5 | 0.865440466 | -1.29104469 | 0.95381823 | 16.2364064 | 1.79054592 | 181.7520694 |
10 | -1 | 0.845 | 0.952 | -1.33 | 14.2 | 1.55 | 167 | 10 | 0.867269282 | -1.305137195 | 0.956043538 | 14.24973176 | 1.546465871 | 166.888929 |
10.5 | -1 | 0.828 | 0.937 | -1.36 | 12.6 | 1.34 | 154 | 10.5 | 0.844737719 | -1.338309611 | 0.935054066 | 12.5682699 | 1.342608295 | 153.5938942 |
11 | -1 | 0.839 | 0.945 | -1.37 | 11.1 | 1.15 | 142 | 11 | 0.852293764 | -1.338837015 | 0.942845287 | 11.13575271 | 1.153365724 | 141.6565405 |
11.5 | -1 | 0.798 | 0.908 | -1.41 | 9.91 | 1.02 | 131 | 11.5 | 0.822451916 | -1.370539998 | 0.915807049 | 9.907986177 | 1.023113579 | 130.9013282 |
12 | -1 | 0.805 | 0.911 | -1.42 | 8.85 | 0.917 | 121 | 12 | 0.831943361 | -1.384756316 | 0.921983468 | 8.849912231 | 0.91731928 | 121.1807115 |
Modules
Human liver cohort, top 5K genes
...