Table V.
Detection of false negatives
The LIMMA procedure was used to compare consecutive sets of concentrations (0.1 cpc against 0 cpc, 1 cpc against 0.1 cpc, etc.). “−1” and “+1” indicate that the gene is flagged by LIMMA as down-regulated or up-regulated, respectively, whereas “0” is used for genes that do not appear to be differentially expressed. All pair-wise comparisons should theoretically be assigned “−1”.
| Spike RNA | 0 vs 0.1 | 0.1 vs 1 | 1 vs 10 | 10 vs 100 | 100 vs 1000 | 1000 vs 10,000 |
|---|---|---|---|---|---|---|
| CATMA | CATMA | CATMA | CATMA | CATMA | CATMA | |
| 1 | 0 | 0 | −1 | −1 | −1 | −1 |
| 2 | 0 | 0 | 0 | −1 | −1 | −1 |
| 3 | −1 | +1 | −1 | −1 | −1 | −1 |
| 4 | 0 | 0 | −1 | −1 | −1 | −1 |
| 5 | −1 | 0 | −1 | −1 | −1 | −1 |
| 6 | +1 | −1 | −1 | −1 | −1 | −1 |
| 7 | 0 | 0 | −1 | −1 | −1 | −1 |
| 8 | 0 | +1 | −1 | −1 | −1 | −1 |
| 9 | 0 | +1 | −1 | −1 | −1 | −1 |
| 10 | 0 | 0 | −1 | −1 | −1 | −1 |
| 11 | 0 | 0 | 0 | −1 | −1 | −1 |
| 12 | 0 | 0 | −1 | −1 | −1 | −1 |
| 14 | 0 | 0 | 0 | −1 | −1 | −1 |
| Agilent | Agilent | Agilent | Agilent | Agilent | Agilent | |
| 1 | 0 | 0 | −1 | −1 | −1 | 0 |
| 2 | 0 | 0 | −1 | −1 | −1 | −1 |
| 3 | 0 | 0 | 0 | −1 | −1 | −1 |
| 4 | 0 | 0 | 0 | −1 | −1 | −1 |
| 5 | 0 | 0 | −1 | −1 | −1 | 0 |
| 7 | 0 | 0 | 0 | −1 | −1 | −1 |
| 8 | −1 | 0 | −1 | −1 | −1 | −1 |
| 9 | 0 | +1 | 0 | 0 | −1 | −1 |
| 10 | 0 | −1 | 0 | −1 | −1 | 0 |
| 11 | −1 | 0 | −1 | −1 | −1 | −1 |
| 12 | 0 | 0 | −1 | −1 | −1 | 0 |
| 14 | 0 | 0 | 0 | −1 | −1 | −1 |