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 SoftwareFor GSEA version 2:
- The latest jar file is available at:
- GSEA requires at least Java 6 but works with Java 7 or Java 8 as well. These are available through DotKit:
$ use Java-1.8
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 foo.gmx -collapse falseIf 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 foo.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.
- 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.