Package Comparison Details, by dataset
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 |
0.231 |
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 |
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
Soft Threshold Choice
Modules
Unequal beta, module diff=33%:
grey turquoise blue brown yellow green black red
grey 2938 4 9 3 4 0 1 5
turquoise 52 346 0 0 0 0 0 0
blue 177 0 197 0 0 0 0 0
brown 155 0 17 0 0 0 0 0
green 134 0 0 1 0 0 0 0
yellow 77 0 0 70 0 0 0 0
red 74 0 0 0 0 58 0 0
pink 30 0 1 0 66 0 0 0
black 58 0 0 51 0 0 0 13
purple 52 0 0 0 0 0 0 0
greenyellow 50 0 0 0 0 0 0 0
tan 49 0 0 0 0 0 0 0
magenta 12 0 0 0 0 0 45 0
salmon 42 0 0 0 0 2 0 0
midnightblue 37 0 0 0 0 0 0 0
lightcyan 36 0 0 0 0 0 0 0
grey60 33 0 0 0 0 0 0 0
cyan 5 0 0 0 0 0 0 33
lightgreen 32 0 0 0 0 0 0 0
lightyellow 31 0 0 0 0 0 0 0
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