...

Push Finish to launch GSEA with the default settings or .

Alternatively, click on the Configure icon to customize access the analysis advanced options (Figure 7). Number of data permutations (needed to calculate the normalised enrichment scores) can be controlled using the Permutations option. Low value filter is turned on by default and will remove all the genes with the lowest average coverage of 1.0 or below (for details please see the GSA chapter) . 

References

1. Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102(43):15545-15550. doi:10.1073/pnas.0506580102
2. Mootha VK, Lindgren CM, Eriksson KF, et al. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003;34(3):267-273. doi:10.1038/ng1180