Welcome to the gsea-help group. This is the official help and discussion forum for Gene Set Enrichment (GSEA) and Molecular Signature Database (MSigDB). Please post questions, bug reports, and suggestions here. If you're having a problem, try searching this list to see if your question has already been addressed. If a suggested solution does not address your issue, please create a new topic. Everyone is encouraged to contribute by suggesting bug fixes, and joining discussions of feature enhancements.

Other resources include:

GSEA / MSigDB web site: www.gsea-msigdb.org.

For scientific questions about the GSEA method, review our 2005 GSEA PNAS paper and 2003 Nature Genetics paper.

For questions about using the software and resolving errors, you may find answers in our FAQ, User Guide, or Documentation Wiki.

For questions about terms of use, see the GSEA and MSigDB license page.

For help with errors in GSEA when accessing CHIP annotation files from the Broad website, please see our FAQ.

Due to changes in our annotation process Clariom Array support CHIP files have been moved to: https://data.broadinstitute.org/gsea-msigdb/msigdb/annotations_legacy/ These legacy annotations target the specified version of MSigDB, but are constructed using a old to new symbol remapping procedure rather than directly from deposited probe-set level annotations.

If you contact us about a problem with the GSEA desktop application, please send us the following information:

The version of GSEA you are using, your computer operating system, and your version of Java.
The text of any error messages, and the log from the GSEA session that caused the error. To retrieve the log, click the [+] icon in the bottom left of the GSEA window and copy the text.
Optionally, example data that demonstrates the problem.

If you do not wish to create a Google account, please note that you can also sign up by sending an email to gsea-help+subscribe@googlegroups.com with "subscribe" as the subject, and that when signing up you can set your account to avoid receiving emails.

Negative enrichment score

Anna Huang