GSEA v4.3.x Release Notes

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GSEA Desktop v4.3.1 (Sep 2022)

GSEA v4.3.1 is a bug-fix release to fix an issue with the species-consistency check when working with local files loaded from the user's computer.

GSEA Desktop v4.3.0 (Sep 2022)

GSEA v4.3.0 is an update to support the new Mouse MSigDB database and our adjusted versioning scheme. See the Mouse 2022.1.Mm release notes and Human 2022.1.Hs release notes for more details about the changes to MSigDB.

Users will notice a change in the tabs of both the Gene Set chooser and the CHIP chooser available from the Run GSEA and Run Preranked screens. These allow selecting either Human or Mouse oriented files from the MSigDB servers, to assist users in both choosing the correct files for their analysis and to ensure they are not improperly mixing these files (e.g. using a Mouse CHIP with a Human GMT, etc). Such mixing of files meant for different species will result in an error when it is detected.

These file choosers will also give a new warning when they detect the mixing of files from different versions of MSigDB, even when the species matches.

We have made the decision for now that GSEA will only make such checks on files coming directly from the MSigDB servers within that session. That is, GSEA will not make these checks on any files loaded from the user's computer through the Load Data screen since we can't guarantee the contents or naming of these files.