Networks dissimilarity measure as it is defined here.

Beta vs M value (-batch, center, plate column and row (BCRC))

0.32

Beta vs M value (-batch, plate column and row (CENTER))

0.27

M value (BCRC) vs M value (CENTER)

0.12

Beta (vertical) vs M value (-batch, center, plate column and row (BCRC)) (horizontal):

Modules,grey,turquoise,blue,brown,yellow,black,pink,magenta,red,purple,greenyellow,tan,green,salmon,midnightblue,cyan,lightcyan,grey60,lightgreen
grey,20981,2126,1039,60,227,108,97,92,89,89,86,85,82,46,42,4,34,33,32
turquoise,787,19,0,552,0,0,0,0,24,0,0,0,0,0,1,39,0,0,0
blue,255,0,8,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
brown,1,0,0,0,242,0,0,0,0,0,0,0,0,0,0,0,0,0,0
yellow,0,0,159,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
green,0,0,0,0,0,0,0,0,0,0,0,0,39,0,0,0,0,0,0
black,32,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
pink,30,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
red,29,6,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0


Beta vs M value (CENTER):

"Modules","grey","turquoise","blue","brown","yellow","green","red","black","pink"
"grey",22469,1726,774,166,2,96,45,41,33
"turquoise",1247,19,0,0,155,0,0,0,1
"blue",259,0,5,0,0,0,0,0,0
"brown",1,0,0,242,0,0,0,0,0
"yellow",0,0,159,0,0,0,0,0,0
"green",0,0,0,0,0,39,0,0,0
"black",32,0,0,0,0,0,0,0,0
"red",30,5,0,0,0,0,0,0,0
"pink",30,0,0,0,2,0,0,0,0

M value (BCRC) vs M value (Center):

"Modules","grey","turquoise","blue","brown","yellow","green","red","black","pink"
"grey",22104,2,1,0,3,3,0,2,0
"turquoise",389,1746,16,0,0,0,0,0,0
"blue",283,2,921,0,0,0,0,0,0
"brown",459,0,0,0,156,0,0,0,0
"yellow",61,0,0,408,0,0,0,0,0
"black",108,0,0,0,0,0,0,0,0
"magenta",92,0,0,0,0,0,0,0,0
"tan",85,0,0,0,0,0,0,0,0
"greenyellow",85,0,0,0,0,0,0,1,0
"green",38,0,0,0,0,83,0,0,0
"red",68,0,0,0,0,0,45,0,0
"pink",59,0,0,0,0,0,0,38,0
"purple",40,0,0,0,0,49,0,0,0
"salmon",46,0,0,0,0,0,0,0,0
"cyan",43,0,0,0,0,0,0,0,0
"midnightblue",9,0,0,0,0,0,0,0,34
"lightcyan",34,0,0,0,0,0,0,0,0
"grey60",33,0,0,0,0,0,0,0,0
"lightgreen",32,0,0,0,0,0,0,0,0

Summary of network modules correlations with clinical traits:

traits

Beta

M value (BCRC)

M value (BCR)

mb

mbc

% variance explained

60-73%

45-80%

45-80%

15-60%

15-66%

number of modules

8

18

8

65

79

survival (P value=0.05)

0

0

0 (red=0.0509)

6

8

primary therapy outcome

0

0

1 (red)

 

 

age

1

6

1

 

 

tumor grade

1

1

0

 

 

tumor stage

0

0

0

 

 

Tumor residual disease

0

1

1

 

 

Chromosomal clustering

2

4

1 (brown)

27

52

Gene Ontology

keratinization

keratinization

keratinization

weak

weak

November 16th, 2011 update: We decided to choose M value as a measure for methylation and normalization -batch, -center, -plate row, -plate column for all further analyses.