MeV v4.3 Released

The MeV development team is proud to announce the release of MeV v4.3.
It is now available for download at the TM4 website, http://www.tm4.org/.
MeV v4.3 Major additions

Gene Set Enrichment Analysis (GSEA) Module
GSEA is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). From Jiang, Z., Gentleman, R., 2007. Extensions to gene set enrichment analysis. Bioinformatics., 23(3):306-13.

Bayesian Estimation of Temporal Regulation (BETR) Module
BETR is a flexible linear random-effects modeling framework that takes into account correlations between samples and sampling times. It is a new empirical Bayes approach that has shown improved results over currently used time-course techniques.

Rank Products Analysis (RP) Module
Rank Products is a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. RP provides a fast and efficient technique that is highly resistant to noise and can reduce the number of replicates needed for reliable results.

Support Data File Downloads
Many of the components of MeV require data in addition to the usual expression and annotation data. Previously, users of MeV have had to provide the data files required by the various modules. This could be a hassle, since downloading, validating and keeping track of these files was a chore. A new feature of MeV allows modules to automatically download the support files they need, provided they are freely available online. These files are cached on the local file system so that MeV can continue to function if an internet connection is not available.

Currently, these functions are used by the modules EASE, TEASE, GSEA and BN. The annotation selection components of MeV's file loaders now also use these functions to download annotation for selected arrays.

Minor Additions

* MeV can now accept the broadcasts of name lists from the Gaggle. For more information on Gaggle, see the Gaggle website (http://gaggle.systemsbiology.net/).
? MeV can now be launched via Java WebStart, with a pre-selected data file loaded. See the MeV page on the TM4 Website for details (http://mev.tm4.org/).
* Many display options, such as element size and color range, are now stored between MeV sessions.
* The TDMS file loader now allows users to select between two-color and single-color array types, rather than "two-color" and "affy or single-color".
* File loaders containing a tabular display of the annotation file to be loaded will color-code the cells of the table. The colors represent the data types the loader will assign to each cell.
* File loaders will attempt to guess the first expression value of a data file, before applying the above color-coding. This guess may be wrong, so users should verify the selection.
* Parser for annotation files provided by Affymetrix integrated with the TDMS file loader
* The Cluster Utilities now allows the option of creating clusters by binning values together.

Bugfixes
* The Search functions will now search annotations loaded with the new annotation model.
* The Cluster Import tool will now allow matching of annotation values from the new annotation model.
* Gaggle broadcasts from R are now correctly received.
* Spot Information Box displays annotations already present in the expression file.