News Archives

• Limits GO files to OBO format. Support for RDF-XML has been dropped as the format we supported was deprecated by the GO consortium. If you need to run analyses using the old XML format you will have to use an older version of ErmineJ.
• Fixes a reported issue with OBO file parsing.
• Miscellaneous minor updates and fixes.

This version adds support for the OBO file format for the Gene Ontology in addition to XML. In the future OBO is likely to be the recommended file type to use for ErmineJ.

We are also taking this opportunity to announce the availability of R support for ErmineJ, with the ErmineR library.

Changes in this version affect the behaviour of the software in a particular gene score situation, where the smallest value is the for the top gene. This is in contrast to the typical inputs which are p-values (for which -log10 transformation is conducted, so large values are ranked highest) or fold-changes or other scores that lead to ranking genes in decreasing order (“bigger is better”). Specifically:

• Fixes a bug in the precision-recall method that caused incorrect results when using such scores.
• A related fix was made to the multifunctionality bias assessments when using such scores.
• Fixes a bug in the display of score distributions in the gene set details window (GUI) when using such scores.

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.

Changes include:

• 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.

• ErmineJ now requires Java 8
• Updated external URLs for GO terms
• Multi-gene-mapping microarray probes listed in Gemma platform annotation files are now ignored by default. This behaviour can be modified through a configuration.
• Changes for compatibility with the new Gemma RESTful API
• Mac OS distribution now a DMG file.

This release fixes several problems reported by users as well as including some documentation updates.

• The “generic” distribution of the software had an error in the configuration causing it to fail to execute.
• The logging configuration was causing some problems for command line use.
• In the details screen, if your “raw data” matrix is missing data matching the rows in your score file, saving the image or data would fail (bug 3898)
• The data matrix reader was skipping the first two columns of data relative to the documented meaning of the “first data column” (bug 3922)
• We reduced use of the term “probe” in favor of the more platform-neutral “element”, to refer to the potential many-to-one relationship between the data and genes.
• There have been some additions and clarifications to the on-line documentation.

This release fixes several issues:

• Quicklists did not correctly deal with genes in your hitlist that are unannotated (are not members of any gene groups).
• Error handling for the “multifunctionality diagnostics” has been improved.
• Problems with selecting score files and poor interaction with the file validation in the Analysis Wizard (bug 3874)
• The ermineJ log file is now stored in your ermineJ.data directory by default, and the location is configurable by editing your ermineJ.properties file. This will help reduce and track down issues some users had with missing log files.