Hi there, I’m wanting to use Broad’s PreRanked GSEA tool on a list of genes and their log2(FC) values to look for enrichment of a number of gene sets (details: FC values based on EdgeR output of RNA-seq data, only significant genes included (FDR < 0.05), no FC cut-offs applied). For this scenario, is it acceptable to use the default ‘weighted’ enrichment statistic (p = 1), or would ‘classic’ (p = 0) be more appropriate? I suspect ‘weighted’ would be OK, but I want to be sure. I’d also appreciate it if anyone can describe how exactly the ‘ranked list metric’ value for each gene is calculated when using PreRanked GSEA (this is unclear to me as there is no phenotype list to determine a correlation from and subsequently calculate the weight of the steps, as in standard GSEA). Thanks so much.
