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GSEA Changelog

What's new in GSEA 2.1.0

Mar 23, 2015
  • In collaboration with the Bader lab at the University of Toronto, we have added Enrichment Map visualization as one of the steps in a GSEA analysis. Enrichment Map visualization organizes gene sets into a network work two gene sets are connected in the enrichment map if they have high overlap, i.e., if they share many of the same genes. Applying automatic layout techniques, groups of inter-related gene sets will tend to cluster together, providing a much easier and intuitive visualization of the enrichment results. For example, the resulting enrichment map might reveal distinct clusters of gene sets associated with the Cell Cycle, Transcription, Translation, DNA Metabolism, etc.
  • There is now a button on GSEA's main user interface for initiating the creation of an enrichment map of GSEA results directly from the GSEA desktop application. Users can create multiple enrichment maps from this interface; they can also compare two different enrichment results within a single map.

New in GSEA 2.0.14 (Jan 24, 2014)

  • GSEA determines format of an input file from its extension. On some computers, system settings silently add .txt extension and do not always make it visible. This causes GSEA program to recognize these files as expression data in TXT format which in these cases might not be correct. In v2.0.13 we addressed this problem by inspecting .txt file names to see if there is a legitimate extension before .txt ending. Recognized extensions included .gct, .res, .pcl, .gmx, .gmt, and .rnk. In this release we have added .cls to the list of recognized file extensions.
  • Improved text describing error 1001. Now reads "After pruning, none of the gene sets passed size thresholds". This communicates that tests to determine whether gene sets pass size threshold are done AFTER gene sets have been pruned to remove genes that do not appear in the gebe expression data file or ranked gene list file.
  • GSEA now uses anonymous FTP to access CHIP files from our FTP server.
  • Updated to use the latest version (version 3.2) of apache commons math library; this eliminates reported conflict with GATK.
  • Added Permissions attribute to GSEA jar file to eliminate security warning triggered by latest (7u51) Java release.