Table 1.
As the threshold stringency increases, the number of known imprinted genes identified as differentially expressed at a q < 0.05 reaches a local optimum while the number of significant genes decreases.
| Effects of filtering at various thresholds on the Affymetrix Human array | ||||||||
| Filter Thresholds | PM Threshold | Number of Probes After Filtering | % Probes After Filtering | % Probe Sets Remaining | Number Significant (q < 0.05) | Number Known Imprinted (q < 0.05) | Number Significant (p adj < 0.05) | Number Known Imprinted (p adj < 0.05) |
| No filter | 0.000 | 604,258 | 100.0% | 100.00% | 21 | 4 | 8 | 2 |
| Median | 7.655 | 361,110 | 59.8% | 99.11% | 20 | 6 | 7 | 2 |
| 75% quartile | 8.479 | 197,484 | 32.7% | 92.80% | 14 | 6 | 4 | 2 |
| 1 standard deviation above mean | 9.104 | 113,455 | 18.8% | 79.20% | 6 | 3 | 3 | 2 |