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. 2008 Jul 4;4(7):e1000115. doi: 10.1371/journal.pgen.1000115

Figure 1. Area under ROC Curves (AUC) for the comparison of Mixed Model, PAGE and GSEA methods using simulated data.

Figure 1

For each scene, there were 20 simulated datasets, each with 1500 genes assigned to 50 gene-sets, among them only the first gene-set (gene-set 1) include genes associated with outcome by design. The test results from each method were compared with true classification of the gene-sets. The AUC measures the ability of a test to correctly classify whether a gene-set is associated with outcome. In scenes 1–9, when genes were shifted in both directions equally (up_p = 0.5), mixed model outperformed both GSEA and PAGE. In scenes 10–18, when most of genes were shifted in one direction (up_p = 0.8), mixed model and PAGE performed similar, and they both outperformed GSEA, especially when the magnitude of differential expression in gene-set 1 is small (scenes 10, 13, 16).