Package Comparison Details
Package Comparison Details, by dataset
- 1 Package Comparison Details, by dataset
- 1.1 Female Mouse Liver (UCLA Tutorial)
- 1.1.1 Modules (3.7% different)
- 1.2 Cranio Dataset
- 1.2.1 Soft Threshold Choice
- 1.2.2 Modules
- 1.3 Colon cancer, top 5K genes
- 1.3.1 Soft Threshold Choice
- 1.3.2 Modules
- 1.4 Human liver cohort, top 5K genes
- 1.5 i.e. 28 are grouped together. The rest are scattered across modules. PARC
- 1.5.1 Modules
- 1.6 Methylation (full set)
- 1.6.1 Soft Threshold Choice
- 1.6.2 Modules
- 1.1 Female Mouse Liver (UCLA Tutorial)
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 |