= A to Z protocol to create an EnrichmentMap from gene expression data and using GSEA (Gene Set Enrichment Analysis) =
 * goal
 * specific goal: known all pathways that could be altered between the 2 (or more) conditions that we are testing. We aim in this analysis to have a global and comprehensive view of what is happening in the cells. Snapshots of entire cells at the moment the RNA was extracted.

 * How to create a rank file (.rnk)
  * the rank file contains only 2 columns. The gene names as the first column and the differential expression values for each gene as the second column. In this protocol, we will use the t value from a moderated Student's t-test. Headers (column names) should be removed. The format should be tab delimited (meaning that the columns are separated by tabs) and the file extension should be .rnk.
  * the rank file is a format described in the GSEA documentation: http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats
  * the rank file will be used to run the gene set enrichment analysis (GSEA).

 * How to get the pathway database file (.gmt)
  * In this protocol we are going to use a file that include pathways from different sources. We observed that 

 * How to run GSEA

 * How to create an expression file
 * How to create a map
 * What is the next step, how to use the map
  * How to create a figure
  * How to interpret the results
  * What next

 * (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 ==
== What is the next step, how to use the map ==