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 1271 147 0 blue 648 373 0 grey 53 0 42	turquoise blue grey turquoise 1958 0 0 blue 0 520 0 grey 14 0 42

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 2655 1 11 0 0 0 blue 23 950 45 102 57 0 brown 24 55 423 1 1 0 yellow 278 4 73 0 0 0 green 0 9 0 125 1 0 grey 0 2 0 61 0 26 red 0 24 0 49 0 0	turquoise blue brown yellow green grey turquoise 2980 0 0 0 0 0 blue 0 997 0 0 0 0 brown 0 0 552 0 0 0 yellow 0 48 0 338 0 0 green 0 0 0 0 59 0 grey 0 0 0 0 0 26

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        16718         4     0    1      4   1     6     8       1      1           0   17
blue           47       226     0    0      0   0     0     0       0      0           0    0
brown          16         0   194    0      0   0     0     0       0      0           0    0
turquoise      80         0     0 185      0   0     3    51       0      0           0    0
yellow         25         0     0    0    114   0     0     0       0      0           0    0
green          26         0     0    5      0 102     0     0       0      0           0    0
red            19         0     0    2      0   0   100     0       0      0           0    0
pink           68         0     0    0      0   0     0     0       0      0           0    0
magenta        11         0     0    0      0   0     0     0      45      0           0    0
black          45        22     0    4      0   0     0    44       0      0           0    0
purple          6         0     0    0      0   0     0     0       0     43           0    0
salmon         36         0     0    0      0   0     0     0       0      0           0    0
greenyellow     6         0     0    0      0   0     0     0       0      0          36    0
tan             2         0     0    0      0   0     0     0       0      0           0   35
cyan           32         0     0    0      0   0     0     0       0      0           0    0

grey turquoise blue brown yellow green black red pink magenta purple greenyellow
grey      17091         3    0     0      0     0     2   2    0       0      1           0
blue         13       247    0     0      0     0     2   0    0       0      0           0
turquoise    21         2 197     0      0   109    99   3    0       0      0           0
brown         0         0    0   194      0     0     0   0    0       0      0           0
yellow        0         0    0     0    118     0     0   0    0       0      0           0
green         3         0    0     0      0     0     0 98    0       0      0           0
black         0         0    0     0      0     0     0   0   52       0      0           0
red           9         0    0     0      0     0     0   0    0      46      0           0
pink          0         0    0     0      0     0     0   0    0       0     43           0
magenta       0         0    0     0      0     0     0   0    0       0      0          36

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     13693    0    0     1     14     0   0    0       0     0      0
grey           1302 8623 757   459    304   116 106   11      40    39     32
blue             42    2 1139     1      2     0   0    0       0     0      0
brown             1    0    0     0      0   277   0    0       0     0      0
green           180    2    0     0      3     0   0    0       0     0      0
yellow           45    0    0    73    100     0   0    0       0     0      0
red              28    0    0    85      3     0   0    0       0     0      0
black             8    0    0     0      0     0   0   51       0     0      0
pink              0    0    0     0      0     0   0    0       0    39      0

turquoise grey blue brown yellow green red black pink magenta purple
turquoise       15263    0    0     0     17     0   0     0    0       0      0
grey                1 8619    2     4      0     0   0     0    0       0      1
blue                0    0 1894     1      1     0   0     0    0       0      0
brown               1    6    0   532      4     0   0     0    0       0      0
yellow             34    1    0     2    404     0   0     0    0       0      0
green               0    0    0     0      0   393   0     0    0       0      0
red                 0    1    0     0      0     0 106     0    0       0      0
black               0    0    0    80      0     0   0     0    0       0      0
pink                0    0    0     0      0     0   0    78    0       0      0
magenta             0    0    0     0      0     0   0     0   62       0      0
purple              0    0    0     0      0     0   0     0    0      40      0
greenyellow         0    0    0     0      0     0   0     0    0       0     31

Package Comparison Details, by dataset

Female Mouse Liver (UCLA Tutorial)

Modules (3.7% different)

Cranio Dataset

Soft Threshold Choice

Modules

Colon cancer, top 5K genes

Soft Threshold Choice

Modules

Human liver cohort, top 5K genes

Modules

Comparison to published results

Comparison of newly run Sage code to published modules:

i.e. 28 are grouped together. The rest are scattered across modules. PARC

Modules

Methylation (full set)

Soft Threshold Choice

Modules

i.e. 28 are grouped together. The rest are scattered across modules.

PARC