Table 6 Type 1 error (when effect size is 0) in simulation studies
From: SNP-PRAGE: SNP-based parametric robust analysis of gene set enrichment
Causal gene set | Gene set size | Gene size | Significance level | Z-statistic method | SNP-PRAGE | GLOSSI | GSEA | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Â | Â | Â | Â | m | m | Â | Â | ||||||||
| Â | Â | Â | Â | 1 | 2 | 3 | 4 | 5 | 1 | 2 | 3 | 4 | 5 | Â | Â |
Set1 | 20 genes | 9~12 SNPs | 0.05 0.01 | .005 .002 | .003 .002 | .004 .003 | .004 .002 | .003 .001 | .057 .013 | .053 .009 | .054 .010 | .054 .011 | .053 .010 | .052 .010 | .051 .011 |
Set2 | 20 genes | 20~30 SNPs | 0.05 0.01 | .083 .033 | .087 .035 | .084 .034 | .080 .031 | .080 .031 | .051 .011 | .052 .011 | .052 .009 | .050 .008 | .052 .008 | .051 .009 | .049 .010 |
Set3 | 20 genes | 36~49 SNPs | 0.05 0.01 | .430 .144 | .641 .294 | .760 .429 | .864 .634 | .891 .671 | .047 .008 | .049 .010 | .050 .010 | .050 .011 | .051 .011 | .049 .011 | .052 .012 |