## page was renamed from Software/EnrichmentMap/GSEATutorial
#acl All:read
{{attachment:Software/EnrichmentMap/UserManual/enrichmentmap_logo3.png|Enrichment Map Logo|align="right"}}<<BR>> 
= Enrichment Map Tutorial Direct from GSEA Interface =
<<TableOfContents(3)>>

== Outline ==

This quick tutorial will guide you through the generation of an Enrichment Map for an analysis performed using [[http://www.broadinstitute.org/gsea/| GSEA Gene Set Enrichment Analysis]] directly from the GSEA interface.  

== To run this tutorial ==
    * You need to have Cytoscape installed : minimally 3.3.0 must be installed ['''cytoscape 3.0 requires Java 8''']
    * You need a version of GSEA that supports the direct creation of Enrichment Maps. '''(GSEA 3.0 or higher)'''
    * '''If you have previously run GSEA analyses you wish to create an Enrichment Map from skip to step 2'''.

<<Include(Software/EnrichmentMap/Tutorial,"Description of the tutorial files contained in the GSEATutorial folder",2, from="^== Description of the tutorial files contained in the GSEATutorial folder ==$", to="== Instructions ==")>>


== Instructions ==
<<Include(Software/EnrichmentMap/Tutorial,"Step 1: Run GSEA",3, from="^=== Step 1: Generate GSEA output files ===$", to="'''Note'''")>>

=== Step 2: Generate Enrichment Map ===
{{attachment:Software/EnrichmentMap/AutoMultiEMFromGSEA/GSEA_EMmulti1.png|Screenshot GSEA-EM Input Panel|align="right"}}
   1. Once GSEA has completed click in the ''Steps in GSEA analysis'' panel click on ''Enrichment Map Visualization''.  When you click on the ''Steps in GSEA analysis'' cytoscape 3.3 or higher should automatically be launched.  It will take a few seconds for cytoscape to load.  If you try and create a network before it is finished initializing GSEA will not be able to communicate with cytoscape yet.  ['''In Cytoscape 3.3.0 the Cyotscape splash screen will not disappear until it has finished initializing but in later version you will be able to configure the Enrichment map parameters within GSEA while cytoscape is initializing''']
   1. Navigate to the analysis or analyses you wish to create an enrichment map for.  There are two ways to do this:
      A. click on the ''...'' next to ''Select a GSEA result from the application cache''.  From the list select the set of analyses to load. (hold down CTRL or COMMAND key to select multiple analyses).  Click on ''OK''.
      B. click on the ''...'' next to ''[OR] Locate a GSEA result folder from the file system''.  Navigate to the GSEA result directory you wish to use.  Click on ''OK''.
   1. Click on ''Load GSEA Results''. '''NOTE: if the GSEA analysis was performed on a dataset that was not collapsed it will take a few seconds for the information to load as it needs to collapse it first.'''
   1.  Bottom frame will appear, auto-populating file fields according to the GSEA results folders specified.  Multiple GSEA folders can be specified.  If more than one folder is specified bottom frame will contain specifications for two datasets.  If only one directory is specified then only one dataset will be accommodated. 
   1.  The user can specify which of the datasets to use as dataset 1 by selecting dataset from drop down list.  Selecting a different dataset will automatically populate ''Expression(Dataset 1) with the corresponding expression file
   1.  If you have conducted a GSEA analysis on a Preranked list of genes but wish to see the original expression file associated with your enrichment map update the path to the expression file next to '''Expression (Dataset 1)'''.
   1.  The user can specify which of the datasets to use as dataset 2 by selecting dataset from drop down list.  Selecting a different dataset will automatically populate ''Expression(Dataset 2) with the corresponding expression file
   1.  If you have conducted a GSEA analysis on a Preranked list of genes but wish to see the original expression file associated with your enrichment map update the path to the expression file next to '''Expression (Dataset 2)'''.

   1. Tune Parameters (check out [[http://baderlab.org/Software/EnrichmentMap/UserManual#Tips_on_Parameter_Choice| tips for choosing parameters]])
      * P-value cut-off `0.001`
      * Q-value cut-off `0.05`
      * Check Overlap Coefficient
         * Overlap coefficient cut-off `0.5`

   1. Click on Build Enrichment Map
   1. Cytoscape should launch and create your Enrichment map.
   1. Go to View, and activate Show Graphics Details 


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<<Include(Software/EnrichmentMap/Tutorial,"Step 3: Examining Results",3, from="^=== Step 3: Examining Results ===$")>>