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Table 3 Results of the analyses of three datasets by GSEA and SAM-GS.

From: Improving gene set analysis of microarray data by SAM-GS

Dataset

% of individual genes with FDR* ≤ 0.25

# of gene sets with FDR ≤ 0.01

# of gene sets with FDR ≤ 0.25

Sensitivity/Specificity (AUC†) of GSEA‡

  

GSEA

SAM-GS

GSEA

SAM-GS

 

Sex

0.1%

4

5

6

6

0.78/0.98 (0.94)

p53

0.3%

3

36

6

308

0.21/0.94 (0.68)

Leukemia

79.9%

0

182

5

182

0.06/NA§ (NA§)

  1. * FDR = False discovery rate estimate
  2. † AUC = Area under the ROC curve
  3. ‡ Taking SAM-GS p ≤ 0.05 as the target to be predicted
  4. § All gene sets in the leukemia dataset had SAM-GS p ≥ 0.05