Table 1 Average Type I error rate (empirical α) when nominal α is 0.05
From: Gene set analyses for interpreting microarray experiments on prokaryotic organisms
Set Size | True mean log-ratio of genes in the set | Standard deviation of log-ratios of genes in the set | GSEA-NR | ABSSUM-NR | SUMSQ-NR | SUM-NR | MAX-MEAN-NR | FET 1/2 | FET 1 | FET 2 | FET 3 |
|---|---|---|---|---|---|---|---|---|---|---|---|
2–5 genes | 0 | 0.01–0.05 | 0.0005 | 0 | 0 | 0.056 | 0 | 0 | 0 | 0 | 0 |
|  |  | 0.10–0.20 | 0.005 | 0.001 | 0.0006 | 0.058 | 0.002 | 0.0004 | 0 | 0 | 0 |
|  | ± 0.05 | 0.01–0.05 | 0.02 | 0 | 0 | 0.056 | 0 | 0 | 0 | 0 | 0 |
|  |  | 0.10–0.20 | 0.01 | 0.002 | 0.0008 | 0.06 | 0.003 | 0.0005 | 0 | 0 | 0 |
10 or more genes | 0 | 0.01–0.05 | 0.29 | 0 | 0 | 0.13 | 0 | 0 | 0 | 0 | 0 |
|  |  | 0.10–0.20 | 0.03 | 0.004 | 0 | 0.14 | 0.0005 | 0.0001 | 0 | 0 | 0 |
|  | ± 0.05 | 0.01–0.05 | 0.45 | 0 | 0 | 0.15 | 0 | 0 | 0 | 0 | 0 |
|  |  | 0.10–0.20 | 0.08 | 0.006 | 0 | 0.15 | 0.004 | 0.0002 | 0 | 0 | 0 |