Table 3.
Percent of shared UniGene ID between Affymetrix and other probe set definitions under different FDR thresholds
| FDR (SAM Q-value) cut-off (%) | <1 | <2 | <5 | <10 | <20 |
|---|---|---|---|---|---|
| UG | 73.0 | 73.0 | 65.1 | 63.9 | 71.6 |
| 3UGa | 75.4 | 75.4 | 67.8 | 63.8 | 68.2 |
| ENTREZG | 64.4 | 54.8 | 64.1 | 62.3 | 71.8 |
| ENSG | 70.9 | 62.3 | 61.7 | 62.0 | 70.5 |
| REFSEQ | 66.0 | 58.1 | 70.4 | 62.2 | 72.2 |
| 3REFSEQa | 67.5 | 67.5 | 67.7 | 64.5 | 70.6 |
| ENST | 69.7 | 52.3 | 67.1 | 64.8 | 71.7 |
| 3ENSTa | 72.9 | 65.6 | 65.8 | 62.9 | 69.2 |
| DOTS | 56.7 | 61.1 | 65.6 | 65.2 | 67.7 |
| 3DOTSa | 60.6 | 61.4 | 65.0 | 65.5 | 69.3 |
aProbe set definition started with ‘3’ are those only containing the most 3′ 11 probes if there are more than 11 probes in a probe set.