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. 2019 Apr 2;15(4):e1006899. doi: 10.1371/journal.pcbi.1006899

Fig 4. Comparison of QuSAGE with directional Fisher’s method, directional Stouffer’s method and the effect-size method.

Fig 4

A) Significant genes sets identified by QuSAGE meta-analysis, directional Fisher’s method, directional Stouffer’s method and the effect-size method. Using the same FDR cutoff of 15%, QuSAGE meta-analysis, directional Fisher’s method, directional Stouffer’s method and the effect-size method identified 11, 16, 27 and 40 significant gene sets respectively. B) Permutation analysis of QuSAGE meta-analysis demonstrates higher specificity than directional Fisher’s method, directional Stouffer’s method and effect-size method. The labels of LR and HR subjects were permutated 2000 times, and meta-analysis was carried out for each of these permuted data sets. For each permutation, the number of false positive gene sets (defined at FDR < 15%) was determined for QuSAGE meta-analysis, directional Fisher’s method, directional Stouffer’s method and the effect-size method. The counts of permutations with and without any false positive results is indicated in the pie charts.