Method | TP | TP rate | TN | FP | FDR | FN |
---|
TaqMan
| 763 | 0 | 85 | 0 | 0 | 0 |
p-t test
| 558 | 73.13 | 55 | 30 | 5.10 | 205 |
p-t test + FDR
| 549 | 71.95 | 56 | 29 | 5.02 | 214 |
p-t test + FC
| 483 | 63.30 | 64 | 21 | 4.17 | 280 |
p-t test +FDR+FC
| 479 | 62.78 | 64 | 21 | 4.20 | 284 |
SAMq
| 508 | 66.58 | 63 | 22 | 4.15 | 255 |
- We use different methods to detect significantly differentially expressed genes for data Quantile normalized: (1) t-test (p-value < 0.05), (2) t-test controlling FDR at 5% level, (3) t-test (p-value < 0.05) and FC < 1.5, (4) t-test controlling FDR at 5% level and FC < 1.5, or (5) SAM q < 0.05. We compare the results for data generated by site 1, from each normalization method, with the ones from TaqMan® assays for which differential expression is detected using t-test and controlling FDR at 5% level. We keep track of up/down regulation in each platform.