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.
- 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.
We are excited to announce a major new release of ErmineJ. There are a number of new features, and overall the software is improved and easier to use. Some highlights:
- Introduction of diagnostics and corrections for “gene multifunctionality”. See the documentation for details.
- Introduction of a new gene set scoring method based on precision-recall. See the documentation for details.
- Numerous user interface improvements have been made including filtering of displays and better error handling.
- Support is much improved for non-GO gene annotation schemes such as MolSigDB or KEGG, and the use of ‘hit lists’ as input is simplified.
- Improved Mac OSX support.
- Much of the code has been rewritten and many minor and major bugs have been fixed. Note that while the existing core algorithms of ErmineJ have not been changed, changes to the way gene annotations are handled may cause differences in results.
We believe this upgrade will increase the future maintainability of the software and sets the stage for the introduction of new features. We look forward to your feedback.
For a more complete change list see the version history
Version 2.1.22 – (November 2010)
Fixes a CLI bug that caused gene score file to be required even when using the correlation method. This only affects users of the command line tool.
Version 2.1.18 – (July 2009) Changes include:
- Fix broken links on GO file documentation page.
- Update our mailing list address. Old subscribers have been subscribed to the new list
- Fix a bug that kept the
-goption working on the command line.
Version 2.1.15 – (July 2007) This is primarily a bugfix release. The most significant changes are:
- An error was made in the two previous distributions: an incorrect jar file was included in the windows installer, so some bugfixes were not correctly included. In particular, an issue with how the GO classes were read in is now consistent between all distributions. Thanks to Oliver Homann for bringing this to our attention.
- There were problems with some command line arguments not being recognized correctly.
- We fixed two bugs that can affect the analysis. First, it was possible for some implicit GO term associations to be missed. This primarily affected large GO categories that most users tend to remove from consideration, but may affect analyses. Second, there was a problem using input scores containing negative values and the “best score” option to handle multiple occurrence of genes on array designs. Users who always use positive values would not be affected by this problem. We thank the users who identified reported these problems!
September 2 2005: Version 2.1.6 – Maintanance release to fix bugs in reading and utilization of user-defined gene sets introduced since 2.1.3.
August 16 2005: Version 2.1.5 – Maintenance release, primarily fixing performance issues. Most importantly, a bug causing slow responses in the tree view after an analysis has been fixed, and the performance of the correlation analysis has been drastically improved.
July 11 2005: Version 2.1.4 – Maintenance release to fix a number of recently discovered issues affecting the user interface, performance, and reading of data files.
June 10 2005: Version 2.1.3 – Maintenance release to fix a variety of bugs, and introduces a few minor new features.
June 7 2005: Version 2.1.2 – New feature: Receiver operator characteristic (ROC) analysis. Also fixes a number of bugs, all users should upgrade.
June 2 2005: Version 2.1.1 – Fixes bugs which caused incorrect parsing of gene descriptions and resulted in multiple custom gene set directories. All users should upgrade.
June 1 2005: Version 2.1 has been released . Many new improvements and changes.
- The command line interface has been largely rewritten and should be more robust, easier to use, and easier to understand.
- A variety of cosmetic and GUI bugs have been fixed, especially affecting Linux and Macintosh users.