Gene Set Enrichment Analysis

GSEA tutorial: Analysis of Microarray Data

Command line options for running GSEA: Syntax

Excerpts from GSEAPreranked Page

1. when using the GSEAPreranked tool, we recommend you provide a ranked list that already has unique human gene symbols and select false for the parameter Collapse data set to gene symbols. 
2. In standard GSEA you can choose to set  the parameter Permutation type to phenotype (the default) or gene set, but this option is not available in GSEAPreranked.
3. In the case of GSEAPreranked, you should make sure that this weighted scoring scheme applies to your choice of ranking statistic. When in doubt, we recommend using a more conservative scoring approach by setting Enrichment statistic to classic.
4. select Tools>GseaPreranked.
5. Gene sets database.
6. Number of permutations. Specify the number of gene_set permutations to perform in assessing the statistical significance of the enrichment score. It is best to start with a small number, such as 10. After the analysis completes successfully, run it again with a full set of permutations. The GSEA recommends 1000 gene_set permutations.