Directionality of GSEA result Vs log2FC

Question

[amitkrj2002]

Hello, I have a question about the directionality of GSEA analysis. RNA seq data analysis for a gene showed -2.06 log2FC with p-value 0.01 in the Knockouts. Performing GSEA on the same Ranklist using GO Mol.Fun dataset shows positive enrichment with the enrichment score in positive. Can the GSEA results determine the real directionality of the gene expression status?

Answer 1

[dsull]

I think there's some confusion.

LogFC describes how an individual gene changes in expression.

GSEA is for analysis of a "gene set" with respect to your expression data, not for analysis of an individual gene.