Table 1.
Type I error rates across the five approaches for the 500 null sets and the 500 nonspurious gene sets
| Pathway method | Across 500 null sets | Across 500 nonspurious gene sets | ||
|---|---|---|---|---|
| Nominal α = 0.05 | Nominal α = 0.005 | Nominal α = 0.05 | Nominal α = 0.005 | |
| No gene-level aggregation | ||||
| WS | 0.492 | 0.190 | 0.043 | 0.004 |
| CMC | 0.232 | 0.054 | 0.037 | 0.003 |
| Gene-level aggregation | ||||
| WS-GSEA | 0.048 | 0.004 | 0.001 | 0.000 |
| WS-KS | 0.040 | 0.003 | 0.000 | 0.000 |
| WS-Fisher | 0.429 | 0.244 | 0.010 | 0.004 |
| CMC-GSEA | 0.063 | 0.007 | 0.002 | 0.000 |
| CMC-KS | 0.044 | 0.004 | 0.004 | 0.000 |
| CMC-Fisher | 0.484 | 0.235 | 0.048 | 0.006 |
WS, weighted sum; CMC, combined multivariate collapsing; GSEA, gene set enrichment analysis; KS, Kolmogorov-Smirnov test; Fisher, Fisher’s combined probability test.