Hi guys, I have a general question regarding the pre-ranked GSEA. I have a list of genes ranked according to the LogFC and then a list of genes that is my geneset. I would like to see if the genes of the geneset are enriched in my ranked list. To do this, I'm running the pre-ranked GSEA. I'm not sure the meaning of NES and FDR. Which is the statistical score to consider to evaluate the enrichment?
Thank you in advance
1 answer
NES stands for normalized enrichment score. It's calculated as the enrichment score value of the pathway divided by the average enrichment score of random gene sets of the same size and the same ES sign.
FDR corrseponds to p-value adjusted to multiple hypothesis comparison. Although, if you use the Broad version, it's not a proper adjustment, so be cautious when using it.
Log in to answer this question.
-
Does Normalized Enrichment Score (NES) from GSEA correlate with gene set upregulation and down regu…
written by grsyhhsb •
-
GSEA p value dependent on pre-ranked list size?
written by garfield320 •
-
How to prepare ranked-gene list for statistical enrichment test in PANTHER database
written by kousi31 •
-
GSEA after MACS2 peak calling for ChIP-seq; want positive enrichment only
written by sonark •
-
clusterProfiler GSEA for upregulated and downregulated gene sets: conflicting results
written by hibernicah •
-
GSEA: Can a gene set have positive and negative enrichment scores?
written by penny.lane •
-
Gene set enrichment analysis
written by Shamim Sarhadi
-
Input all the ranked genes into pre-ranked GSEA?
written by blairzxy •
-
Input GSEA Pre-ranked list
written by stevenlang123
-
question about GSEA
written by kanwarjag
