...
| Power | 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 | -1 | 0.707 | 0.991 | 1.18 | 700 | 700 | 1120 |
| 1 | 1 | 0.737 | 1.14 | 0.994 | 700 | 700 | 1120 |
2 | 1.5 | -1 | 0.231 | 0.969 | 0.332 | 440 | 424 | 840 |
| 2 | 1.5 | 0.252 | 0.298 | 0.979 | 440 | 424 | 840 |
3 | 2 | -1 | 0.0114 | 0.903 | -0.136 | 296 | 269 | 668 |
| 3 | 2 | 0.12 | -0.164 | 0.917 | 296 | 269 | 668 |
4 | 2.5 | -1 | 0.523 | 0.921 | -0.444 | 209 | 178 | 549 |
| 4 | 2.5 | 0.623 | -0.491 | 0.901 | 209 | 178 | 549 |
5 | 3 | -1 | 0.749 | 0.914 | -0.66 | 153 | 120 | 463 |
| 5 | 3 | 0.788 | -0.683 | 0.904 | 153 | 120 | 463 |
6 | 3.5 | -1 | 0.819 | 0.892 | -0.798 | 115 | 83.7 | 399 |
| 6 | 3.5 | 0.863 | -0.857 | 0.889 | 115 | 83.7 | 399 |
7 | 4 | -1 | 0.864 | 0.892 | -0.918 | 89.5 | 59.4 | 351 |
| 7 | 4 | 0.895 | -0.952 | 0.894 | 89.5 | 59.4 | 351 |
8 | 4.5 | -1 | 0.884 | 0.888 | -1.01 | 70.9 | 42.2 | 313 |
| 8 | 4.5 | 0.906 | -1.04 | 0.887 | 70.9 | 42.2 | 313 |
9 | 5 | -1 | 0.879 | 0.872 | -1.08 | 57.3 | 30.5 | 283 |
| 9 | 5 | 0.917 | -1.09 | 0.894 | 57.3 | 30.5 | 283 |
10 | 5.5 | -1 | 0.887 | 0.878 | -1.12 | 47.1 | 22.6 | 258 |
| 10 | 5.5 | 0.903 | -1.13 | 0.876 | 47.1 | 22.6 | 258 |
11 | 6 | -1 | 0.872 | 0.864 | -1.14 | 39.3 | 16.8 | 237 |
| 11 | 6 | 0.894 | -1.14 | 0.872 | 39.3 | 16.8 | 237 |
12 | 6.5 | -1 | 0.853 | 0.849 | -1.16 | 33.2 | 12.5 | 220 |
| 12 | 6.5 | 0.877 | -1.17 | 0.861 | 33.2 | 12.5 | 220 |
13 | 7 | -1 | 0.849 | 0.857 | -1.16 | 28.5 | 9.75 | 205 |
| 13 | 7 | 0.868 | -1.17 | 0.863 | 28.5 | 9.75 | 205 |
14 | 7.5 | -1 | 0.836 | 0.861 | -1.16 | 24.7 | 7.44 | 193 |
| 14 | 7.5 | 0.869 | -1.16 | 0.888 | 24.7 | 7.44 | 193 |
15 | 8 | -1 | 0.831 | 0.873 | -1.15 | 21.6 | 5.73 | 182 |
| 15 | 8 | 0.86 | -1.15 | 0.89 | 21.6 | 5.73 | 182 |
16 | 8.5 | -1 | 0.807 | 0.87 | -1.15 | 19.1 | 4.43 | 172 |
| 16 | 8.5 | 0.84 | -1.15 | 0.89 | 19.1 | 4.43 | 172 |
17 | 9 | -1 | 0.78 | 0.858 | -1.14 | 17 | 3.49 | 164 |
| 17 | 9 | 0.828 | -1.13 | 0.896 | 17 | 3.49 | 164 |
18 | 9.5 | -1 | 0.792 | 0.889 | -1.11 | 15.3 | 2.75 | 156 |
| 18 | 9.5 | 0.825 | -1.1 | 0.912 | 15.3 | 2.75 | 156 |
19 | 10 | -1 | 0.782 | 0.906 | -1.09 | 13.9 | 2.18 | 149 |
| 19 | 10 | 0.806 | -1.09 | 0.915 | 13.9 | 2.18 | 149 |
20 | 10.5 | -1 | 0.759 | 0.897 | -1.07 | 12.7 | 1.74 | 143 |
| 20 | 10.5 | 0.8 | -1.08 | 0.921 | 12.7 | 1.74 | 143 |
21 | 11 | -1 | 0.747 | 0.902 | -1.06 | 11.6 | 1.4 | 138 |
| 21 | 11 | 0.789 | -1.06 | 0.933 | 11.6 | 1.4 | 138 |
22 | 11.5 | -1 | 0.752 | 0.914 | -1.04 | 10.7 | 1.14 | 133 |
| 22 | 11.5 | 0.779 | -1.04 | 0.935 | 10.7 | 1.14 | 133 |
23 | 12 | -1 | 0.743 | 0.924 | -1.01 | 9.91 | 0.926 | 128 |
| 23 | 12 | 0.779 | -1.02 | 0.947 | 9.91 | 0.926 | 128 |
...
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 |
...
The publication says beta was set to 5.5, not 11. So we reran the Sage code with that beta:
grey blue turquoise brown yellow green red black pink magenta
grey 971 0 0 0 0 0 0 0 0 0
blue 4 617 0 0 0 0 0 0 0 0
brown 0 0 602 0 0 0 0 0 0 0
turquoise 170 0 0 439 0 0 75 0 0 0
yellow 5 0 347 0 0 0 0 0 0 0
green 0 0 272 0 0 0 0 0 0 0
red 39 0 0 0 192 0 0 0 0 0
magenta 148 0 0 0 0 0 0 0 0 0
black 126 0 0 12 0 0 0 0 70 0
pink 58 0 0 0 0 106 0 0 0 0
purple 0 0 104 0 0 0 0 0 0 0
tan 80 0 0 0 0 0 0 0 0 0
greenyellow 18 0 0 0 0 0 0 71 0 0
salmon 59 0 0 0 0 0 0 0 0 0
cyan 56 0 0 0 0 0 0 0 0 0
midnightblue 0 0 0 0 0 0 0 0 0 55
lightcyan 45 0 0 0 0 0 0 0 0 0
lightgreen 44 0 0 0 0 0 0 0 0 0
grey60 44 0 0 0 0 0 0 0 0 0
lightyellow 39 0 0 0 0 0 0 0 0 0
coral 38 0 0 0 0 0 0 0 0 0
sienna 0 0 36 0 0 0 0 0 0 0
gold 36 0 0 0 0 0 0 0 0 0
peru 34 0 0 0 0 0 0 0 0 0
and still got 18% difference in module membership. Checking the P450 genes:
NOT P450
grey 966 5
turquoise 682 2
blue 621 0
brown 591 11
yellow 349 3
green 244 28
red 231 0
black 208 0
pink 164 0
magenta 148 0
purple 101 3
greenyellow 89 0
tan 80 0
salmon 59 0
cyan 56 0
midnightblue 55 0
lightcyan 45 0
lightgreen 44 0
grey60 44 0
lightyellow 39 0
coral 38 0
sienna 34 2
peru 34 0
gold 34 2
i.e. 28 are grouped together. The rest are scattered across modules.
The regression statistics for selecting beta are below, where "Cut" is the value of beta and "Adj R^2" is the value which should exceed a chosen threshold. When the threshold is set to the nominal value of 0.90 , beta=11 is the smallest value for which "Adj R^2" exceeds the threshold. The value of 5.5 would be selected if the threshold were set to 0.80.
Cut | p-value | Adj R^2 | Truncated Adj R^2 | slope | mean(k) | median(k) | max(k) |
|---|---|---|---|---|---|---|---|
1 | -1 | 0.12 | 0.871 | 0.841 | 949 | 939 | 1640 |
1.5 | -1 | -0.0707 | 0.854 | -0.11 | 508 | 486 | 1110 |
2 | -1 | 0.164 | 0.895 | -0.688 | 294 | 268 | 787 |
2.5 | -1 | 0.41 | 0.939 | -1.03 | 181 | 156 | 583 |
3 | -1 | 0.554 | 0.953 | -1.28 | 117 | 94.7 | 445 |
3.5 | -1 | 0.656 | 0.966 | -1.47 | 79 | 59.7 | 347 |
4 | -1 | 0.713 | 0.973 | -1.58 | 54.9 | 38.4 | 276 |
4.5 | -1 | 0.76 | 0.981 | -1.67 | 39.3 | 25.3 | 223 |
5 | -1 | 0.786 | 0.983 | -1.72 | 28.8 | 17 | 182 |
5.5 | -1 | 0.801 | 0.983 | -1.75 | 21.5 | 11.7 | 150 |
6 | -1 | 0.821 | 0.987 | -1.78 | 16.4 | 8.33 | 125 |
6.5 | -1 | 0.825 | 0.979 | -1.79 | 12.7 | 6.04 | 104 |
7 | -1 | 0.824 | 0.969 | -1.8 | 10 | 4.5 | 88.1 |
7.5 | -1 | 0.83 | 0.971 | -1.8 | 8.03 | 3.35 | 74.8 |
8 | -1 | 0.835 | 0.977 | -1.79 | 6.52 | 2.54 | 63.9 |
8.5 | -1 | 0.843 | 0.983 | -1.77 | 5.36 | 1.93 | 54.8 |
9 | -1 | 0.849 | 0.984 | -1.74 | 4.45 | 1.53 | 47.2 |
9.5 | -1 | 0.845 | 0.975 | -1.72 | 3.75 | 1.22 | 40.9 |
10 | -1 | 0.859 | 0.976 | -1.66 | 3.19 | 0.994 | 35.5 |
10.5 | -1 | 0.873 | 0.973 | -1.61 | 2.74 | 0.835 | 31 |
11 | -1 | 0.904 | 0.98 | -1.53 | 2.38 | 0.694 | 27.1 |
11.5 | -1 | 0.907 | 0.983 | -1.53 | 2.08 | 0.564 | 24.7 |
12 | -1 | 0.877 | 0.963 | -1.58 | 1.84 | 0.462 | 23.4 |
We reran the Sage code with beta=5.5:
grey blue turquoise brown yellow green red black pink magenta
grey 971 0 0 0 0 0 0 0 0 0
blue 4 617 0 0 0 0 0 0 0 0
brown 0 0 602 0 0 0 0 0 0 0
turquoise 170 0 0 439 0 0 75 0 0 0
yellow 5 0 347 0 0 0 0 0 0 0
green 0 0 272 0 0 0 0 0 0 0
red 39 0 0 0 192 0 0 0 0 0
magenta 148 0 0 0 0 0 0 0 0 0
black 126 0 0 12 0 0 0 0 70 0
pink 58 0 0 0 0 106 0 0 0 0
purple 0 0 104 0 0 0 0 0 0 0
tan 80 0 0 0 0 0 0 0 0 0
greenyellow 18 0 0 0 0 0 0 71 0 0
salmon 59 0 0 0 0 0 0 0 0 0
cyan 56 0 0 0 0 0 0 0 0 0
midnightblue 0 0 0 0 0 0 0 0 0 55
lightcyan 45 0 0 0 0 0 0 0 0 0
lightgreen 44 0 0 0 0 0 0 0 0 0
grey60 44 0 0 0 0 0 0 0 0 0
lightyellow 39 0 0 0 0 0 0 0 0 0
coral 38 0 0 0 0 0 0 0 0 0
sienna 0 0 36 0 0 0 0 0 0 0
gold 36 0 0 0 0 0 0 0 0 0
peru 34 0 0 0 0 0 0 0 0 0
and still got 18% difference in module membership. Checking the P450 genes:
NOT P450
grey 966 5
turquoise 682 2
blue 621 0
brown 591 11
yellow 349 3
green 244 28
red 231 0
black 208 0
pink 164 0
magenta 148 0
purple 101 3
greenyellow 89 0
tan 80 0
salmon 59 0
cyan 56 0
midnightblue 55 0
lightcyan 45 0
lightgreen 44 0
grey60 44 0
lightyellow 39 0
coral 38 0
sienna 34 2
peru 34 0
gold 34 2
i.e. 28 are grouped together. The rest are scattered across modules.
PARC
Modules
Unequal beta, module diff=4.7% | identical beta, module diff=0.6% |
|---|---|
grey turquoise brown blue yellow red green black magenta purple greenyellow pink | grey turquoise blue brown yellow green black red pink magenta purple greenyellow |
Methylation (full set)
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 | -0.00512 | -0.0562 | 0.247 | 2120 | 2230 | 3640 | 1 | 0.039759972 | 0.169460948 | -0.042121587 | 7249.755797 | 7583.706845 | 12508.45604 |
1.5 | -1 | 0.0167 | 0.413 | -0.215 | 1410 | 1350 | 2880 | 1.5 | 0.140389955 | -0.269553255 | 0.59303507 | 4828.992487 | 4542.145536 | 10029.03836 |
2 | -1 | 0.184 | 0.688 | -0.366 | 1020 | 845 | 2400 | 2 | 0.276562808 | -0.390168503 | 0.631322022 | 3491.738926 | 2824.215768 | 8386.544599 |
2.5 | -1 | 0.257 | 0.645 | -0.414 | 778 | 541 | 2040 | 2.5 | 0.362446542 | -0.458433391 | 0.523661313 | 2655.348672 | 1808.299631 | 7173.887246 |
3 | -1 | 0.323 | 0.563 | -0.453 | 611 | 356 | 1760 | 3 | 0.42871745 | -0.515750913 | 0.431061197 | 2086.334341 | 1176.893287 | 6223.960796 |
3.5 | -1 | 0.386 | 0.51 | -0.49 | 491 | 238 | 1540 | 3.5 | 0.46604534 | -0.560354757 | 0.369873339 | 1676.348853 | 781.2514422 | 5452.12826 |
4 | -1 | 0.451 | 0.509 | -0.516 | 401 | 160 | 1350 | 4 | 0.493523645 | -0.60630005 | 0.358279952 | 1368.885142 | 527.8374153 | 4809.805129 |
4.5 | -1 | 0.504 | 0.513 | -0.545 | 331 | 112 | 1190 | 4.5 | 0.51122219 | -0.643452727 | 0.371756376 | 1131.587843 | 368.4541959 | 4266.321824 |
5 | -1 | 0.542 | 0.521 | -0.577 | 276 | 81 | 1050 | 5 | 0.522934331 | -0.681405777 | 0.399981701 | 944.5030783 | 259.4558865 | 3800.880221 |
5.5 | -1 | 0.571 | 0.536 | -0.608 | 232 | 57.9 | 939 | 5.5 | 0.532765178 | -0.72250099 | 0.440336737 | 794.5816675 | 186.1875426 | 3398.594443 |
6 | -1 | 0.588 | 0.556 | -0.636 | 196 | 42.3 | 838 | 6 | 0.543038666 | -0.754901305 | 0.481364519 | 672.8857753 | 135.1591844 | 3048.3654 |
6.5 | -1 | 0.612 | 0.591 | -0.664 | 167 | 30.8 | 750 | 6.5 | 0.546592526 | -0.787367292 | 0.521630192 | 573.065346 | 99.6082135 | 2741.653967 |
7 | -1 | 0.635 | 0.628 | -0.688 | 143 | 23 | 673 | 7 | 0.546688103 | -0.824100826 | 0.556997344 | 490.4753338 | 72.92787987 | 2471.728523 |
7.5 | -1 | 0.634 | 0.646 | -0.724 | 123 | 17.1 | 606 | 7.5 | 0.540586249 | -0.867631489 | 0.58655908 | 421.6371568 | 54.2456294 | 2233.179306 |
8 | -1 | 0.652 | 0.682 | -0.744 | 106 | 12.7 | 547 | 8 | 0.548418618 | -0.896985225 | 0.619099353 | 363.8954176 | 40.26400042 | 2021.591247 |
8.5 | -1 | 0.646 | 0.691 | -0.776 | 91.5 | 9.69 | 494 | 8.5 | 0.564768173 | -0.919427493 | 0.659981637 | 315.1907849 | 30.24453177 | 1833.315466 |
9 | -1 | 0.65 | 0.714 | -0.803 | 79.5 | 7.35 | 448 | 9 | 0.571866178 | -0.945524396 | 0.689291949 | 273.9048972 | 22.6602808 | 1665.30474 |
9.5 | -1 | 0.633 | 0.716 | -0.84 | 69.2 | 5.47 | 406 | 9.5 | 0.573099177 | -0.977455448 | 0.712350288 | 238.7515604 | 17.41343565 | 1514.991934 |
10 | -1 | 0.625 | 0.727 | -0.867 | 60.5 | 4.25 | 369 | 10 | 0.578839688 | -1.000683008 | 0.734565322 | 208.6986492 | 13.25463367 | 1380.198191 |
10.5 | -1 | 0.626 | 0.742 | -0.893 | 53 | 3.29 | 336 | 10.5 | 0.588455603 | -1.026903911 | 0.755386914 | 182.9109323 | 10.10196054 | 1259.062284 |
11 | -1 | 0.643 | 0.769 | -0.905 | 46.5 | 2.61 | 306 | 11 | 0.597054452 | -1.052133963 | 0.775670911 | 160.707503 | 7.788443435 | 1149.985372 |
11.5 | -1 | 0.657 | 0.79 | -0.926 | 40.9 | 2.05 | 279 | 11.5 | 0.608963051 | -1.071230234 | 0.793960474 | 141.5296132 | 6.067481982 | 1051.587206 |
12 | -1 | 0.669 | 0.809 | -0.941 | 36.1 | 1.57 | 255 | 12 | 0.605496603 | -1.104019616 | 0.800156429 | 124.9160557 | 4.734398295 | 962.6709874 |
Modules
Unequal beta, module diff=14% | Identical beta, module diff=0.2% |
|---|---|
turquoise grey blue brown yellow green red pink magenta black purple | turquoise grey blue brown yellow green red black pink magenta purple |