Gsea at the Broad

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This page describes how to use GSEA from the command line on the Broad UNIX system.
It applies only to researchers at the Broad institute. 

GSEA Software

For GSEA version 2:

  • The latest jar file is available at:
    /xchip/cogs/gsea/gsea2.jar<br />
  • GSEA requires at least Java 7 but Java 8 is preferred.  These are available through DotKit:
    $ use Java-1.8

Command Lines

If your dataset and gene sets already match, use the following command line to run GSEA:

java -Xmx1024m -cp /xchip/cogs/gsea/gsea2.jar xtools.gsea.Gsea -res foo.gct -cls foo.cls -gmx -collapse false 

If you want to use gene symbol based gene sets and your dataset is in some probe set format:

java -Xmx1024m -cp /xchip/cogs/gsea/gsea2.jar xtools.gsea.Gsea -res foo.gct -cls foo.cls -gmx -chip HG_U133A

Note: For the -chip parameter, specify just the name and not the path. For the full list of supported chips, see /xchip/projects/vdb/annotations.

Analysis Results

  • By default, the output is written to a folder in the current working directory with a date prefix.
  • Change the output folder by specifying the -out parameter.
  • Change the name of the report by specifying the -rpt_label parameter.
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