This update mostly affects the command line interface (CLI), but has some impact on the GUI. This includes removing some rarely-used methods, changing some defaults, and renaming some options. This may break (or change the output of) existing scripts using the CLI which is why we have bumped the version number to 3.1.
- The CLI now has an option for limiting analysis for GO aspects such as biological process (as already existed for the GUI)
- The CLI option to save the configuration to a file (-S) now works as intended
- The CLI has an option to set the random seed (-seed) (used for resampling-based approaches)
- CLI and GUI options for turning off multifunctionality assessment are removed (now always true).
- CLI option to set “filter non-specific” is removed (always true)
- CLI multiple test correction methods are renamed “FDR” and “FWE”
- CLI: The “Westfall-Young” multiple test correction method is no longer supported
- Support for alternative annotation file formats has been dropped.
- The options that are no longer supported in the CLI are also ignored when present in configuration files
- Default class size limits are now 20 and 200 (rather than 10 and 100).
- Fix for a bug in retrieving annotation files from Gemma via the GUI.
- Various fixes to the documentation.