Package Comparison Details, by dataset
Cranio Dataset
Soft Threshold Choice
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 power table (The optimum chosen by each is highlighted)
...
...
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
...
| Table of Contents |
|---|
Female Mouse Liver (UCLA Tutorial)
Modules (3.7% different)
blue green brown red turquoise yellow grey black pink magenta purple greenyellow tan salmon cyan midnightblue lightcyan grey60
turquoise 522 0 0 0 0 171 0 0 0 0 0 0 0 0 0 0 0 0
blue 0 373 0 0 0 0 0 0 0 0 0 0 0 0 39 0 0 0
brown 0 0 358 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
yellow 0 0 0 331 0 0 0 0 0 0 0 0 0 0 0 0 0 0
green 0 0 0 0 323 0 0 0 0 0 0 0 0 0 0 0 0 0
red 0 0 0 0 0 256 0 0 0 0 0 0 0 0 0 0 0 0
black 0 0 0 0 203 0 0 0 0 0 0 0 0 0 0 0 0 0
grey 0 0 0 0 0 0 168 0 0 0 0 0 0 0 0 0 0 0
pink 0 0 0 0 0 0 0 134 0 0 0 0 0 0 0 0 0 0
magenta 0 0 0 0 0 0 0 0 122 0 0 0 0 0 0 0 0 0
purple 0 0 0 0 0 0 0 0 0 120 0 0 0 0 0 0 0 0
greenyellow 0 0 0 0 0 0 0 0 0 0 99 0 0 0 0 0 0 0
tan 0 0 0 0 0 0 0 0 0 0 0 86 0 0 0 0 0 0
salmon 0 0 0 0 0 0 0 0 0 0 0 0 76 0 0 0 0 0
cyan 0 0 72 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
midnightblue 0 0 0 0 0 0 0 0 0 0 0 0 0 43 0 0 0 0
lightcyan 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 37 0 0
grey60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 0
lightgreen 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 33
Cranio Dataset
Soft Threshold Choice
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 / Package power table (The optimum chosen by each is highlighted)
...
| 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 | 0.819 231 | 0.892 969 | - 0.798 332 | 115 440 | 83.7 424 | 399 840 |
| 6 2 | 3 1.5 | 0.863 252 | - 0.857 298 | 0.889 979 | 115 440 | 83.7 424 | 399 840 | ||||||
7 3 | 4 2 | -1 | 0.8640114 | 0.892903 | -0.918136 | 89.5 | 59.4 | 351 296 | 269 | 668 |
| 7 3 | 4 2 | 0.895 12 | -0.952 164 | 0.894 917 | 89.5 | 59.4 | 351 | 8 | 4 296 | 269 | 668 |
4 | 2.5 | -1 | 0.884 523 | 0.888 921 | -10.01 444 | 70.9 | 42.2 | 313 209 | 178 | 549 |
| 8 4 | 4 2.5 | 0.906623 | -10.04491 | 0.887901 | 70.9 | 42.2 | 313 | 9 | 5 209 | 178 | 549 |
5 | 3 | -1 | 0.879 749 | 0.872 914 | -10.08 66 | 57.3 | 30.5 | 283 153 | 120 | 463 |
| 9 5 5 | 3 | 0.917 788 | -10.09 683 | 0.894 904 | 57.3 | 30.5 | 283 | 10 | 5 153 | 120 | 463 |
6 | 3.5 | -1 | 0.887 819 | 0.878 892 | -10.12 798 47 | .1 115 | 22 83.6 7 | 258 399 |
| 10 6 | 5 3.5 | 0.903 863 | -10.13 857 | 0.876 889 47.1 | 115 | 22 83.6 7 | 258 399 | ||||||
11 7 | 6 4 | -1 | 0.872 864 | 0.864 892 | -10.14 918 | 3989.3 5 | 1659.8 4 | 237 351 |
| 11 7 | 6 4 | 0.894 895 | -10.14 952 | 0.872 894 | 39 89.3 5 | 16 59.8 4 | 237 351 | ||||||
12 8 | 6 4.5 | -1 | 0.853 884 | 0.849 888 | -1.16 01 | 33 70.2 9 | 12 42.5 2 | 220 313 |
| 12 8 | 64.5 | 0.877 906 | -1.17 04 | 0.861 887 | 3370.2 9 | 1242.5 2 | 220 313 | ||||||
13 9 | 7 5 | -1 | 0.849 879 | 0.857 872 | -1.16 08 | 28 57.5 3 | 9 30.75 5 | 205 283 |
| 13 9 | 7 5 | 0.868 917 | -1.17 09 | 0.863 894 | 28 57.5 3 | 9 30.75 5 | 205 283 | ||||||
14 10 | 7 5.5 | -1 | 0.836 887 | 0.861 878 | -1.16 12 | 24 47.7 1 | 7 22.44 6 | 193 258 |
| 14 10 | 7 5.5 | 0.869 903 | -1.16 13 | 0.888 876 | 24 47.7 1 | 7 22.44 6 | 193 258 | ||||||
15 11 | 8 6 | -1 | 0.831 872 | 0.873 864 | -1.15 14 | 21 39.6 3 | 5 16.73 8 | 182 237 |
| 15 11 | 8 6 | 0.86 894 | -1.15 14 | 0.89 872 | 21 39.6 3 | 5 16.73 8 | 182 237 | ||||||
16 12 | 8 6.5 | -1 | 0.807 853 | 0.87 849 | -1.15 16 | 19 33.1 2 | 4 12.43 5 | 172 220 |
| 16 12 | 8 6.5 | 0.84 877 | -1.15 17 | 0.89 861 | 19 33.1 2 | 4 12.43 5 | 172 220 | ||||||
17 13 | 9 7 | -1 | 0.78 849 | 0.858 857 | -1.14 16 | 17 28.5 | 3 9.49 75 | 164 205 |
| 17 13 | 9 7 | 0.828 868 | -1.13 17 | 0.896 863 | 17 28.5 | 3 9.49 75 | 164 205 | ||||||
18 14 | 9 7.5 | -1 | 0.792 836 | 0.889 861 | -1.11 16 | 15 24.3 7 | 2 7.75 44 | 156 193 |
| 18 14 | 9 7.5 | 0.825 869 | -1.1 16 | 0.912 888 | 15 24.3 7 | 2 7.75 44 | 156 193 | ||||||
19 15 | 10 8 | -1 | 0.782 831 | 0.906 873 | -1.09 15 | 13 21.9 6 | 2 5.18 73 | 149 182 |
| 19 15 | 10 8 | 0.806 86 | -1.09 15 | 0.915 89 | 13 21.9 6 | 2 5.18 73 | 149 182 | ||||||
20 16 | 10 8.5 | -1 | 0.759 807 | 0.897 87 | -1.07 15 | 12 19.7 1 | 1 4.74 43 | 143 172 |
| 20 16 | 10 8.5 | 0.8 84 | -1.08 15 | 0.921 89 | 12 19.7 1 | 1 4.74 43 | 143 172 | ||||||
21 17 | 11 9 | -1 | 0.747 78 | 0.902 858 | -1.06 14 11. | 6 17 | 1 3.4 49 | 138 164 |
| 21 17 | 11 9 | 0.789 828 | -1.06 13 | 0.933 896 11.6 | 17 | 1 3.4 49 | 138 164 | ||||||
22 18 | 11 9.5 | -1 | 0.752 792 | 0.914 889 | -1.04 11 | 10 15.7 3 | 1 2.14 75 | 133 156 |
| 22 18 | 11 9.5 | 0.779 825 | -1.04 1 | 0.935 912 | 10 15.7 3 | 1 2.14 75 | 133 156 | ||||||
23 19 | 12 10 | -1 | 0.743 782 | 0.924 906 | -1.01 09 | 13.9 .91 | 0 2.926 18 | 128 149 |
| 23 19 | 12 10 | 0.779 806 | -1.02 09 | 0.947 915 | 13.9 .91 | 2.18 | 149 | ||||||
20 | 10.5 | -1 | 0.926 759 | 128 |
Both algorithms try to find the lowest power whose R^2 is above the given threshold (0.90). If no power achieves the threshold then the threshold is decremented repeatedly by 0.05 until a solution is found. Since the Sage version finds a maximum of 0.887, it carries out the decrementing procedure. The UCLA version finds three values just above 0.90, and picks the lowest.
Modules
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
Modules
Human liver cohort, top 5K genes
Soft Threshold Choice
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 |
Both algorithms try to find the lowest power whose R^2 is above the given threshold (0.90). If no power achieves the threshold then the threshold is decremented repeatedly by 0.05 until a solution is found. Since the Sage version finds a maximum of 0.887, it carries out the decrementing procedure. The UCLA version finds three values just above 0.90, and picks the lowest.
Modules
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
Unequal beta, module diff=11% | Identical beta, module diff=0.5% |
|---|---|
turquoise blue brown yellow green grey | turquoise blue brown yellow green grey |
Human liver cohort, top 5K genes
Modules
Identical beta, module diff=1.0%
grey turquoise blue brown yellow green red black
grey 3573 0 0 0 0 0 0 0
turquoise 30 730 0 0 0 0 0 0
blue 0 0 261 0 0 0 0 0
brown 0 0 0 136 0 0 0 0
yellow 0 0 0 0 100 0 0 0
green 0 0 0 0 0 88 0 0
red 0 0 0 0 0 0 51 0
black 0 0 0 0 0 0 0 43
Comparison to published results
Module membership of P450 genes in the published Genome Research paper (as gathered from the supplemental materials):
NOT P450
grey 2005 9
turquoise 1314 47
blue 617 0
brown 451 0
yellow 192 0
green 106 0
red 75 0
black 71 0
pink 70 0
magenta 55 0
i.e. 47/56 are grouped into a single module and the remaining 6 are in no module.
Comparison of newly run Sage code to published modules:
grey turquoise brown blue green yellow red pink black magenta
grey 2006 677 259 250 106 104 71 70 48 12
turquoise 4 680 7 16 0 0 2 0 21 0
blue 4 2 2 253 0 0 0 0 0 0
brown 0 2 132 0 0 0 2 0 0 0
yellow 0 0 0 98 0 0 0 0 2 0
green 0 0 0 0 0 88 0 0 0 0
red 0 0 51 0 0 0 0 0 0 0
black 0 0 0 0 0 0 0 0 0 43
There is 39% difference. Checking the P450 genes:
NOT P450
grey 3580 23
turquoise 697 33
blue 261 0
brown 136 0
yellow 100 0
green 88 0
red 51 0
black 43 0
only 33 are grouped together, the remaining ones are unclustered.
The publication says beta was set to 5.5, not 11. 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 |