Table 1.
Ten simulated scenarios for designs D1–3 and D1–5
| Scenario | Proportion | Proportion | Correlation | Log-fold | Hypothesis |
|---|---|---|---|---|---|
| up | down | change | tested | ||
| 1 | 1.00 | 0.00 | 0.0 | 0.1 (0.02) | up |
| 2 | 1.00 | 0.00 | 0.1 | 0.2 (0.2) | up |
| 3 | 0.25 | 0.00 | 0.0 | 0.3 (0.07) | up |
| 4 | 0.25 | 0.00 | 0.1 | 0.4 (0.2) | up |
| 5 | 0.50 | 0.50 | 0.0 | 0.2 (0.07) | mixed |
| 6 | 0.50 | 0.50 | 0.1 | 0.2 (0.2) | mixed |
| 7 | 0.20 | 0.20 | 0.0 | 0.3 (0.1) | mixed |
| 8 | 0.20 | 0.20 | 0.1 | 0.4 (0.2) | mixed |
| 9 | 0.00 | 0.00 | 0.0 | 0.0 (0.0) | up/mix |
| 10 | 0.00 | 0.00 | 0.1 | 0.0 (0.0) | up/mix |
Fold-changes are for 40 genes per set (or 1000 genes per set). Genes regulated in the same direction are positively correlated, those in opposite directions are negatively correlated. In Scenario 10, the correlation applies to all genes in the set. Scenarios differ according to the proportion of up- and down-regulated genes in the set and the intergene correlation.