Table 2 Area under ROC curves up to 100 false positives, MAS5, PPLR, BGX, and Logit-T
From: Empirical Bayes models for multiple probe type microarrays at the probe level
Method | Pre-processing | Affymetrix U95 | Affymetrix 133A | Golden Spike | Gene Logic Tonsil | Gene Logic AML |
|---|---|---|---|---|---|---|
LMW | MAS5 | 89(1) | 87(1) | 60(1) | 79(1) | 70(2) |
IBMT | MAS5 | 87(2) | 87(2) | 59(2) | 77(3) | 69(3) |
LPE | MAS5 | 84(3) | 84(3) | 57(3) | 78(2) | 79(1) |
WAME | MAS5 | 71(6) | 81(5) | 34(5) | 69(4) | 54(8) |
SAM | MAS5 | 74(4) | 81(4) | 11(8) | 67(5) | 54(9) |
LIMMA | MAS5 | 71(7) | 81(6) | 31(6) | 67(6) | 54(6) |
Shrink-t | MAS5 | 71(8) | 80(7) | 23(7) | 67(7) | 54(7) |
t-test | MAS5 | 73(5) | 76(8) | 39(4) | 60(9) | 47(10) |
Efron-t | MAS5 | 65(9) | 72(9) | 3(9) | 66(8) | 57(4) |
FC | MAS5 | 56(10) | 61(10) | 0(10) | 58(10) | 55(5) |
BGX | - | - | 58 | - | 75* | |
logit-T | 94 | 92 | - | 80 | 79 | |
PPLR | multi-mgMOS | 88 | 90 | 57 | 71 | 69 |
# of genes | 12626 | 22029 | 14010 | 12626 | 12626 | |
# of spikes | 16 | 42 | 1331 | 11 | 11 | |
# of groups | 20 | 14 | 2 | 12 | 10 |