Table 2 The proportion of DE genes ( p 1 = 0.05), AUC, and pAUC with a FPR ≤ 0.2 estimated by the t-test, Limma, SAM, and EB approaches (EB-LNN, eGG, eLNN, GaGa) and the β -EB approach averaged over 50 simulated datasets: the case of small sample
From: β-empirical Bayes inference and model diagnosis of microarray data
t | Limma | SAM | eGG | eLNN | GaGa | EB-LNN | β-EB | |
|---|---|---|---|---|---|---|---|---|
In absence of outliers | ||||||||
p 1 | - | - | - | 0.0489 | 0.0430 | 0.0482 | 0.0502 | 0.0518 |
- | - | - | (0.0010) | (0.0009) | (0.0009) | (0.0009) | (0.0009) | |
AUC | 0.9688 | 0.9707 | 0.9675 | 0.9721 | 0.9614 | 0.9780 | 0.9780 | 0.9781 |
(0.0026) | (0.0023) | (0.0023) | (0.0023) | (0.0023) | (0.0016) | (0.0016) | (0.0016) | |
pAUC | 0.1858 | 0.1865 | 0.1849 | 0.1858 | 0.1839 | 0.1873 | 0.1870 | 0.1872 |
(0.0009) | (0.0008) | (0.0008) | (0.0007) | (0.0009) | (0.0007) | (0.0007) | (0.0007) | |
p 1 | - | - | - | 0.0936 | 0.1153 | 0.1106 | 0.0451 | 0.0529 |
- | - | - | (0.0013) | (0.0010) | (0.0012) | (0.0010) | (0.0009) | |
AUC | 0.9466 | 0.9487 | 0.9452 | 0.9352 | 0.9235 | 0.9444 | 0.9626 | 0.9740 |
(0.0030) | (0.0028) | (0.0030) | (0.0027) | (0.0025) | (0.0020) | (0.0018) | (0.0017) | |
pAUC | 0.1773 | 0.1766 | 0.1733 | 0.1591 | 0.1477 | 0.1595 | 0.1769 | 0.1839 |
(0.0010) | (0.0011) | (0.0009) | (0.0011) | (0.0009) | (0.0009) | (0.0008) | (0.0008) | |
In presence of 10% contaminated genes with extreme outliers | ||||||||
p 1 | - | - | - | 0.0919 | 0.1210 | 0.1167 | 0.0379 | 0.0523 |
- | - | - | (0.0011) | (0.0010) | (0.0011) | (0.0009) | (0.0009) | |
AUC | 0.9399 | 0.9418 | 0.9439 | 0.9347 | 0.9145 | 0.9344 | 0.9447 | 0.9766 |
(0.0036) | (0.0035) | (0.0034) | (0.0024) | (0.0029) | (0.0020) | (0.0025) | (0.0016) | |
pAUC | 0.1740 | 0.1716 | 0.1710 | 0.1569 | 0.1413 | 0.1512 | 0.1668 | 0.1859 |
(0.0011) | (0.0012) | (0.0012) | (0.0009) | (0.0009) | (0.0008) | (0.0011) | (0.0007) | |
In presence of 20% contaminated genes with mild outliers | ||||||||
p 1 | - | - | - | 0.1398 | 0.1883 | 0.1725 | 0.0435 | 0.0522 |
- | - | - | (0.0016) | (0.0011) | (0.0013) | (0.0010) | (0.0009) | |
AUC | 0.9208 | 0.9213 | 0.9214 | 0.9049 | 0.8825 | 0.9099 | 0.9301 | 0.9710 |
(0.0035) | (0.0034) | (0.0035) | (0.0027) | (0.0030) | (0.0024) | (0.0022) | (0.0018) | |
pAUC | 0.1678 | 0.1617 | 0.1595 | 0.1335 | 0.1120 | 0.1304 | 0.1510 | 0.1818 |
(0.0011) | (0.0014) | (0.0013) | (0.0012) | (0.0011) | (0.0011) | (0.00126) | (0.0009) | |
In presence of 20% contaminated genes with extreme outliers | ||||||||
p 1 | - | - | - | 0.1380 | 0.2001 | 0.1832 | 0.0343 | 0.0535 |
- | - | - | (0.0029) | (0.0011) | (0.0012) | (0.0009) | (0.0009) | |
AUC | 0.9103 | 0.9109 | 0.9162 | 0.8877 | 0.8680 | 0.8914 | 0.9122 | 0.9753 |
(0.0043) | (0.0041) | (0.0040) | (0.0031) | (0.0032) | (0.0027) | (0.0032) | (0.0016) | |
pAUC | 0.1633 | 0.1561 | 0.1565 | 0.1195 | 0.1018 | 0.1163 | 0.1434 | 0.1840 |
(0.0013) | (0.0015) | (0.0013) | (0.0017) | (0.0010) | (0.0010) | (0.0015) | (0.0008) | |