Table 1 Type I error rates under different settings when the gene-gene correlation ranges from 0 (independence) to mild correlation (ρ=0.3), and when data were generated from GSE48091 to preserve the correlation in real application
From: Probabilistic prioritization of candidate pathway association with pathway score
50 genes per set | 100 genes per set | |||||||
|---|---|---|---|---|---|---|---|---|
ρ=0 | ρ=0.1 | ρ=0.3 | GSE48091 | ρ=0 | ρ=0.1 | ρ=0.3 | GSE48091 | |
Bayesian | 0.023 | 0.022 | 0.022 | 0.035 | 0.024 | 0.022 | 0.022 | 0.025 |
Logistic (ps) | 0.043 | 0.045 | 0.046 | 0.066 | 0.041 | 0.040 | 0.041 | 0.060 |
Logistic (sum) | 0.040 | 0.040 | 0.040 | 0.160 | 0.036 | 0.036 | 0036 | 0.041 |
GSEA | 0.047 | 0.047 | 0.048 | 0.069 | 0.039 | 0.046 | 0.045 | 0.042 |
Global | 0.031 | 0.030 | 0.033 | 0.131 | 0.047 | 0.046 | 0.050 | 0.159 |
ORA | 0.096 | 0.094 | 0.091 | 0.069 | 0.057 | 0.058 | 0.060 | 0.085 |
Fisher’s | 0.048 | 0.048 | 0.052 | 0.163 | 0.049 | 0.049 | 0.049 | 0.201 |