[TM4-Announce] MeV v4.3 Released

[Announcements for the TM4 Microarray Software Suite (http://www.tm4.org/)]

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/.

Please visit the TM4 Forums to get help or suggest improvements to the 
program: http://www.tm4.org/forum/

Please consider filling out the MeV Survey. Doing so will let us know 
the things you do and don't like about MeV.
http://www.surveymonkey.com/s.aspx?sm=SW8XJGJh_2byyKgpRDSOdY3w_3d_3d


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.


Questions? Comments?
Please let us know in the new TM4 forums.
http://www.tm4.org/forum/

Thank you for using MeV
The MeV Team