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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 | --- | --- | --- | --- | 6.5 | 6.5 | YES | 3.7% |
Cranio | 2534 | 249 | --- | --- | --- | --- | 4.0 | 4.5 | YES | 44% / 0.9%* |
Methylation, top 5K genes | 5000 | 555 | --- | --- | --- | --- | 8.5 | 8.5 | YES | 0 |
Colon cancer, top 5K genes | 5000 | 322 | --- | --- | --- | --- | 3 | 3.5 | YES | 11% / 0.5%* |
Human liver cohort, top 5K genes | 5000 | 427 | --- | --- | --- | --- | 6.5 | 5.5 | YES | 33% / 0* |
Methylation (full set)** | 27,578 | 555 | 24h:45m | 180GB | 13h:20m | 196GB | 8 | 11.5 |
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Colon cancer, top 40K genes** | 40,000 | 322 | Out of memory*** | --- | --- | --- | --- | --- | --- | --- |
Human liver cohort** | 40,102 | 427 | Out of memory*** | --- | --- | --- | --- | --- | --- | --- |
* Force beta in Package to match beta in Sage code.
** These were run on an Amazon Elastic Compute Cloud (EC2) "High-Memory Quadruple Extra Large" unix server, having 68GB of RAM.
*** Note: UCLA-WGCNA package also runs out of memory. (An alternative is to use the WGCNA preprocessing step of K-means decomposition, which has been shown to work with >50K genes.)
Note: We skip the performance evaluation for the small data sets.
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