Page Comparison

Networks dissimilarity measure as it is defined [here|http://florence.acadiau.ca/collab/hugh_public/index.php?title=R:compare_partitions].
| 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):
{csv}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{csv}
Beta vs M value (CENTER):
{csv}"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
{csv}

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

{csv}"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
{csv}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.*