GSEA with duplicate sample

Question

[biology_inform]

Hi all, I have a data which is coming from RNA-Seq and it is composed of 2 replicates for each sample. So when I am trying to run GSEA it gives me an error about "phenotype" option even though I run in "gene set" option. The question I would like to ask is that; Which options should I use for this setup?

Answer 1

[jv]

when I am trying to run GSEA it gives me an error about "phenotype" option

Unless you are running the Preranked method you will need to define the "phenotype" (i.e. condition/treatment label) of the expression data set that is used as input. This phenotype information is defined in a plain text file. See https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideTEXT.htm#_Introduction and https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideTEXT.htm#_Phenotype_Labels