Table 3 Simulation setups. Under each setup, there are 5000 genes. Table 3 shows how the genes were simulated. For example, under setup 1, the first 100 genes were generated from N(0,1) and N(3,1) under experimental conditions 1 and 2, respectively, the middle 4800 genes were generated from N(0,1) regardless of experimental condition and the last 100 genes were generated from N(0,1) and N(-3,1) under experimental conditions 1 and 2, respectively. The third column displays the ratio of induced to repressed genes. If the number of repressed genes is 0, the ratio is defined as ∞.
Setup | Genes First/middle/last | Ratio | Experimental condition 1 | Experimental condition 2 | |
|---|---|---|---|---|---|
1 | Â | 100/4800/100 | 1/1 | N(0,1)/N(0,1)/N(0,1) | N(3,1)/N(0,1)/N(-3,1) |
2 | (i) | 200/4800/0 | ∞ |  |  |
| Â | (ii) | 167/4800/33 | 5/1 | Â | Â |
| Â | (iii) | 160/4800/40 | 4/1 | Â | Â |
| Â | (iv) | 100/4800/100 | 1/1 | N(0,1)/N(0,1)/N(0,1) | N(1,1)/N(0,1)/N(-3,1) |
3 | (i) | 0/4600/400 | 0 | Â | Â |
| Â | (ii) | 66/4600/334 | 1/5 | Â | Â |
| Â | (iii) | 80/4600/320 | 1/4 | Â | Â |
| Â | (iv) | 200/4600/200 | 1/1 | Â | Â |