Table 1 Performance of GSEA and SAM-GS on Test 1. Proportions of randomly generated null gene sets that are identified by each method to be associated with the phenotype (p-value ≤ 0.05) in a mouse-microarray study.
From: Improving gene set analysis of microarray data by SAM-GS
Correlation range from which gene-set members were selected (% of individual genes in the range) [% of individual genes in the range with FDR ≤ 0.01] | Methods | Set Size | |||
|---|---|---|---|---|---|
| Â | Â | 10 | 30 | 50 | 100 |
|r| < 0.01 (.9% of all genes are in the range) [0% with FDR≤0.01] | GSEA | 100% | 100% | 100% | 100% |
| Â | SAM-GS | 0% | 0% | 0% | 0% |
|r| < 0.02 (2% of all genes are in the range) [0% with FDR≤0.01] | GSEA | 100% | 100% | 100% | 100% |
| Â | SAM-GS | 0% | 0% | 0% | 0% |
|r| < 0.05 (4% of all genes are in the range) [0% with FDR≤0.01] | GSEA | 100% | 100% | 100% | 100% |
| Â | SAM-GS | 0% | 0% | 0% | 0% |
|r| < 0.1 (8% of all genes are in the range) [0% with FDR≤0.01] | GSEA | 100% | 100% | 100% | 100% |
| Â | SAM-GS | 0% | 0% | 0% | 0% |
|r| < .2 (16% of all genes are in the range) [0% with FDR≤0.01] | GSEA | 96% | 100% | 100% | 100% |
| Â | SAM-GS | 0% | 0% | 0% | 0% |
|r| < .3 (25% of all genes are in the range) [0% with FDR≤.01] | GSEA | 13% | 100% | 100% | 100% |
| Â | SAM-GS | 0% | 0% | 0% | 0% |
|r| < .4 (36% of all genes are in the range) [0% with FDR≤.01] | GSEA | 8% | 100% | 100% | 100% |
| Â | SAM-GS | 0% | 0% | 0% | 0% |
|r| < .5 (47% of all genes are in the range) [0% with FDR≤.01] | GSEA | 0% | 24% | 100% | 100% |
| Â | SAM-GS | 0% | 0% | 0% | 0% |