For Pre-Ranked GSEA on gene and log2FC list: Choose Weighted or Classic Enrichment Statistic?
0
0
Entering edit mode
22 months ago

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.

GSEA RNA-Seq • 1.3k views
ADD COMMENT

Login before adding your answer.

Traffic: 2478 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6