Package Comparison Details, by dataset

Table of Contents

Female Mouse Liver (UCLA Tutorial)

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	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

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Unequal beta, module diff=44%	identical 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

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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

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Unequal beta, module diff=11%	identical 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

Soft Threshold Choice

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Cut

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p-value

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Adj R^2

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Truncated Adj R^2

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slope

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mean(k)

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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	-0.0645 00512	-0.877 0562	0.289 247	632 2120	622 2230	1080 3640	1	1	0.0123 039759972	0.288 169460948	-0.883 042121587	632	622	1080 7249.755797	7583.706845	12508.45604
1.5	-1	- 0.0291 0167	0.911 413	-0.454 215	283 1410	272 1350	611	2 2880	1.5	0.0733 140389955	-0.581	0.905	283	272	611 269553255	0.59303507	4828.992487	4542.145536	10029.03836
2	-1	0.149 184	0.935 688	-0.972 366	140 1020	131 845	367	3 2400	2	0.227 276562808	-0.993 390168503	0.947 631322022	140	131	367 3491.738926	2824.215768	8386.544599
2.5	-1	0.296 257	0.953 645	-10.29 414	74.3	66.5	231	4	778	541	2040	2.5	0.398 362446542	-10.38 458433391	0.965	74.3	66.5	231 523661313	2655.348672	1808.299631	7173.887246
3	-1	0.416 323	0.956 563	-10.53 453	41.9	35.5	150	5 611	356	1760	3	0.543 42871745	-10.75 515750913	0.964 431061197	41 2086.9 334341	35 1176.5 893287	150 6223.960796
3.5	-1	0.535 386	0.968 51	-10.67 49	24.9	19.9	100	6 491	238	1540	3.5	0.63 46604534	-10.86 560354757	0.966	24.9	19.9	100 369873339	1676.348853	781.2514422	5452.12826
4	-1	0.675 451	0.977 509	-10.57 516	15.4	11.5	68.9	7 401	160	1350	4	0.761 493523645	-10.71 60630005	0.984 358279952	15 1368.4 885142	11 527.5 8374153	68 4809.9 805129
4.5	-1	0.767 504	0.961 513	-10.96 545	9.86	6.94	57.2	8	331	112	1190	4.5	0.817 51122219	-20.05 643452727	0.956 371756376	9 1131.86 587843	6 368.94 4541959	57 4266.2 321824
5	-1	0.832 542	0.95 521	-20.14 577	6.53	4.33	48.7	9 276	81	1050	5	0.852 522934331	-20.18 681405777	0.93 399981701	6 944.53 5030783	4 259.33 4558865	48 3800.7 880221
5.5	-1	0.888 571	0.951 536	-20.15 608 4	.46 232	2 57.74 41.9	10 939	5.5	0.904532765178	-20.1972250099	0.95440336737	4 794.465816675	2 186.741875426	41 3398.9594443
6	-1	0.892 588	0.927 556	-20.15 636	3.12	1.8	36 196	42.3	11 838	6	0.912 543038666	-20.17 754901305	0.931 481364519	3 672.12 8857753	1 135.8 1591844	36 3048.3 3654
6.5	-1	0.907612	0.922591	-20.11664 2.24	167	1 30.2	31.6	12 8	750	6.5	0.951 546592526	-20.07 787367292	0.958 521630192	2 573.24 065346	1 99.2 6082135	31 2741.6 653967
7	-1	0.926 635	0.935 628	-20.04 688	1.65	0.821	27.7	13	143	23	673	7	0.943 546688103	-20.02 824100826	0.942 556997344	1 490.65 4753338	0 72.821 92787987	27 2471.7 728523
7.5	-1	0.925 634	0.929 646	-10.98	1.23	0.568	24.4	14 724	123	17.1	606	7.5	0.967 540586249	-10.92 867631489	0.962 58655908	1 421.23 6371568	0 54.568 2456294	24 2233.4 179306
8	-1	0.923 652	0.923 682	-1.91 0.945 744 0.394	106	2112.6 7	15 547	8	0.964 548418618	-10.85 896985225	0.956 619099353 0	363.945 8954176	0 40.394 26400042	21 2021.6 591247
8.5	-1	0.927 646	0.924 691	-1.85 0.737 776 0	91.276 5	19 9.1 69	16 494	8.5	0.978 564768173	-10.77 919427493	0.972 659981637 0	315.737 1907849	0 30.276 24453177	19 1833.1 315466
9	-1	0.949 65	0.946 714	-10.77 803 0	79.585 5	0 7.196 35	17	17 448	9	0.979 571866178	-10.7 945524396	0.973 689291949 0	273.585 9048972	0 22.196 6602808	17 1665.30474
9.5	-1	0.964 633	0.961 716	-1.69 0.472 84 0	69.141 2 15	5.2 47	18 406	9.5	0.976 573099177	-10.65 977455448	0.969 712350288 0	238.472 7515604	0 17.141 41343565	15 1514.2 991934
10	-1	0.962 625	0.958 727	-1.63 0.387 867 0	60.101 5	13 4.6 25	19 369	10	0.974 578839688	-1.58 000683008	0.967 734565322 0	208.387 6986492	0 13.101 25463367 13	1380.6 198191
10.5	-1	0.942 626	0.938	-1.59	0.322	0.0741	12.2	20 742	-0.893	53	3.29	336	10.5	0.971 588455603	-1.54 026903911	0.962 755386914 0	182.322 9109323	0 10.0741 10196054	12 1259.2 062284
11	-1	0.933 643	0.928 769	-10.54 905 0	46.272 5	0 2.0546 61	11 306	21	11	0.988 597054452	-1.47 052133963	0.985 775670911 0	160.272 707503	0 7.0546 788443435	11 1149.985372
11.5	-1	0.935 657	0.93	-1.49	0.232	79	-0.0404 926	40.9	2.96 05	22 279	11.5	0.989 608963051	-1.42 071230234	0.986 793960474 0	141.232 5296132	06.0404 067481982	91051.96 587206
12	-1	0.92 669	0.913 809	-1.45 0.201 941 0	36.0297 1	9 1.02 57	23 255	12	0.991 605496603	-1.37 104019616	0.988 800156429 0	124.201 9160557	0 4.0297 734398295	9 962.02 6709874

Modules

Unequal beta, module diff=

...

14%	Identical beta, module diff=0.2%
turquoise grey blue brown yellow green

...

Methylation (full set)

Soft Threshold Choice

...

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

Versions Compared

Old Version 9

New Version Current

Key

Package Comparison Details, by dataset

Female Mouse Liver (UCLA Tutorial)

Human liver cohort, top 5K genes

Soft Threshold Choice

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

Methylation (full set)

Soft Threshold Choice

Page Comparison

Versions Compared

Old Version 9

New Version Current

Key

Package Comparison Details, by dataset

Female Mouse Liver (UCLA Tutorial)

Human liver cohort, top 5K genes

Soft Threshold Choice

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

Methylation (full set)

Soft Threshold Choice

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

PARC