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
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. 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.
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 |
Add Comment