= Protocol = * A to Z protocol to create an EnrichmentMap from gene expression data and using GSEA (Gene Set Enrichment Map) * How to create a rank file * How to create an expression file * How to run GSEA * How to create a map * What is the next step, how to use the map * How to preprocess the data using R * How to preprocess the data using Excel = FIRST EXAMPLE WITH AFFYMETRIX MICROARRAY DATA == == step1: installation == * 1) install R (http://www.r-project.org/) * 2) install RStudio (http://www.rstudio.com/) * 3) Go through on online R tutorial (e.g. this one: http://www.cyclismo.org/tutorial/R/) == How to preprocess the data (normalization, QC, differential expression) == == How to update the annotations == How to create a rank file == == How to create an expression file == == How to run GSEA == == How to create a map == == What is the next step, how to use the map ==