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
- description of the data
Download the data from GEO
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