Summary and networks comparison
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):
Beta vs M value (CENTER):
M value (BCRC) vs M value (Center):
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) |
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age | 1 | 6 | 1 |
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tumor grade | 1 | 1 | 0 |
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tumor stage | 0 | 0 | 0 |
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Tumor residual disease | 0 | 1 | 1 |
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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.