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Dataset | # Probes | # Samples |
| Sage Time | Sage Space | Package Time | Package Space | Sage Beta | Package Beta | Gene trees same? | Module difference (%) |
|---|---|---|---|---|---|---|---|---|---|---|---|
Female mouse liver | 3600 | 135 |
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Methylation (gene subset) | ?? | 555 |
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Colon cancer (small gene subset) | ?? | 322 |
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Cranio | 2534 | 249 |
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Methylation (full set) | 27,578 | 5555 |
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Colon cancer (large gene subset) |
| 322 |
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Human liver cohort | 40,102 | 427 |
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compute correlation coefficient | |||||||||||
determine optimal value for beta | |||||||||||
compute TOM | |||||||||||
perform hierarchical clustering over TOM (using 'hclust') | |||||||||||
detect and label modules in TOM (using 'cutreeDynamic') |
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Note: We skip the performance evaluation for the small data sets.