Table 3. Overall optimality calls for TCGA data, including both COMMUNAL and the TCGA clustering assignments. For COMMUNAL output, if two values for K both showed repeated optima, both are listed.
| COMMUNAL major optima | COMMUNAL minor optima | COMMUNAL optima @ 1500 genes | Broad Analysis consensus NMF | Broad Analysis consensus hierarchical | |
|---|---|---|---|---|---|
| BRCA | 2 | 6 & 7 | 2 & 6 | 8 | 5 |
| COADREAD | 2 | None | 2 | 4 | 4 |
| GBM | 2 | 4 & 5 | 2 & 5 | 4 | 4 |
| KIRC | 2 | 4 | 2 & 4 | 3 | 7 |
| LUSC | 2 | 5 & 6 | 2 & 5 | 4 | 3 |
| OV | None | 3 & 6 | 6 | 3 | 3 |
| UCEC | 2 | 6 | 2 & 6 | 4 | 5 |
Note that the two TCGA consensus clustering methods (NMF and hierarchical) agree in only three cases.
For COMMUNAL output, if two values for K both showed repeated optima, both are listed