GSEA v2.0.14. Release Notes

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GSEA v2.0.14 has the following upgrades:
  1. 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.
  2. 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.
  3. GSEA now uses anonymous FTP to access CHIP files from our FTP server.
  4. Updated to use the latest version (version 3.2) of apache commons math library; this eliminates reported conflict with GATK.
  5. Added Permissions attribute to GSEA jar file to eliminate security warning triggered by latest (7u51) Java release.
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