Several gene set enrichment methods are available, the most famous/popular is the Broad Institute tool. Many other tools are available (See for example the biocView of GSE which list 82 different packages). There are several parameters in consideration :
- the statistic used to order the genes,
- if it competitive or self-contained,
- if it is supervised or not,
- and how is the enrichment score calculated.
I am using the fgsea - Fast Gene Set Enrichment Analysis package to calculate the enrichment scores and someone told me that the numbers are different from the ones on the Broad Institute despite all the other parameters being equivalent.
Are these two methods (fgsea and Broad Institute GSEA) equivalent to calculate the enrichment score?
I looked to the algorithms of both papers, and they seem fairly similar, but I don't know if in real datasets they are equivalent or not.
Is there any article reviewing and comparing how does the enrichment score method affect to the result?