https://divingintogeneticsandgenomics.com/tags/gsea/ Recent content in GSEA on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Mon, 01 Aug 2016 19:52:00 -0700 https://divingintogeneticsandgenomics.com/archive/gene-set-enrichment-analysis-gsea-explained/ Mon, 01 Aug 2016 19:52:00 -0700 https://divingintogeneticsandgenomics.com/archive/gene-set-enrichment-analysis-gsea-explained/ I was asked to do a Gene Set Enrichment Analysis (GSEA) for RNA-seq data. One of the most popular tool is GSEA from broad Institute. To better understand the underlying method of GSEA, I read the original paper: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles and searched on biostars. I quote from the biostar post: so, to run GSEA you have your list of genes (L) and two conditions (or more), i. https://divingintogeneticsandgenomics.com/archive/using-awk-to-format-the-gene-expression-file-to-gct-format-for-gene-set/ Tue, 19 May 2015 13:42:00 -0700 https://divingintogeneticsandgenomics.com/archive/using-awk-to-format-the-gene-expression-file-to-gct-format-for-gene-set/ After one runs microarray or RNA-seq analysis, usually he would do a Gene Set Enrichment Analysis (GSEA) analysis. There are many tools to use. One of the most commonly used one is GSEA developed in Broad Institute. It requires four data files to be loaded: 1. Expression dataset in res, gct, pcl or txt format 2. Phenotype labels in cls format 3. Gene sets in gmx or gmt formt 4. Chip annotations