From: Improving gene set analysis of microarray data by SAM-GS
Pearson correlation of genes in the gene set with the phenotype | Methods | Set Size | |||
---|---|---|---|---|---|
 |  | 10 | 30 | 50 | 100 |
Half of genes with |r| ≥ .4, the other half with |r| < .4 | GSEA | 1% | 3% | 0% | 1% |
 | SAM-GS | 93% | 100% | 100% | 100% |
Half of genes with |r| ≥ .5 the other half with |r| < .5 | GSEA | 3% | 4% | 3% | 1% |
 | SAM-GS | 100% | 100% | 100% | 100% |
Half of genes with |r| ≥ .6, the other half with |r| < .6 | GSEA | 6% | 7% | 7% | 18% |
 | SAM-GS | 100% | 100% | 100% | 100% |
Half of genes with |r| ≥ .7 the other half with |r| < .7 | GSEA | 12% | 18% | 31% | 66% |
 | SAM-GS | 100% | 100% | 100% | 100% |
Half of genes with |r| ≥ .8, the other half with |r| < .8 | GSEA | 20% | 64% | 88% | 100% |
 | SAM-GS | 100% | 100% | 100% | 100% |
Half of genes with |r| ≥ .9, the other half with |r| ≥ .9 | GSEA | 69% | 100% | 100% | 100% |
 | SAM-GS | 100% | 100% | 100% | 100% |