|  | FDR50 | FDR | True Positive | False Positive |
---|
R
|
p var
|
RDAM
|
SAM
|
RDAM
|
SAM
|
RDAM
|
SAM
|
RDAM
|
SAM
|
2R
|
0.3
| 55% | 63% | 33% | - | 4 | - | 2 | - |
 |
0.1
| 25% | 49% | 21% | - | 172 | - | 45 | - |
 |
0.05
| 9% | 39% | 11% | 14% | 281 | 23 | 35 | 4 |
 |
0.01
| 1% | 26% | 15% | 23% | 452 | 175 | 77 | 51 |
3R
|
0.3
| 42% | 47% | 17% | - | 55 | - | 11 | - |
 |
0.1
| 7% | 28% | 16% | 20% | 344 | 156 | 64 | 40 |
 |
0.05
| 3% | 19% | 13% | 18% | 409 | 246 | 60 | 54 |
 |
0.01
| 0% | 11% | 14% | 22% | 473 | 381 | 80 | 109 |
5R
|
0.3
| 17% | 21% | 18% | 25% | 261 | 264 | 58 | 88 |
 |
0.1
| 2% | 4% | 15% | 20% | 455 | 395 | 81 | 101 |
 |
0.05
| 0% | 2% | 16% | 20% | 472 | 419 | 87 | 106 |
 |
0.01
| 0% | 0% | 19% | 19% | 474 | 443 | 111 | 105 |
- Comparisons were made between two groups of two replicates. The first group is composed of synthetic data sets made from the experimental replicates Wt-t0a and Wt-t0b, in which 1000 genes (500 increased and 500 decreased) are changed, and the second group is composed of synthetic data sets without extra variation. Results are shown for increased genes. The first column (R), indicates the number of replicates used. The second column (p var), gives the p-value of the extra variation introduced to the changed genes. The third column displays the FDR50, and the fourth column (FDR) the real FDR corresponding to the set of genes selected at FDR = 20%. For the same level of selection, columns 5 and 6 give, respectively, the number of true and false positives.