...
Networks
...
dissimilarity
...
measure
...
as
...
it
...
is
...
defined
...
...
.
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):
...
...
M value (BCRC) vs M value (Center):
...
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.