[TM4-Announce] MeV v4.5 is released

Fri Nov 13 10:38:42 MST 2009

The MeV development group is proud to announce the release of MeV v4.5. 
Please visit http://mev.tm4.org/ to download it.

Release Notes:

MeV v4.5 release
November 13, 2009

MeV is now provided under the conditions of the Artistic License v2.0. 
It was previously released under the Artistic License v1.0.

Major additions

R project
MeV has integrated a R (CRAN) hook where by R functions and libraries 
can be called within the Java instance using shared libraries. Mev 
developed a library around the JRI (rForge) API which uses JNI, to make 
this happen. The user in *most cases would not have to set up or 
configure anything to run R dependent modules and it should be 
completely transparent. Please also note that MeV does not produce a 
command line interface to run R commands. This integration was done to 
leverage the R environment where many algorithms are readily available 
and does not need to be re-implemented in Java. MeV would use R 
internally as appropriate and the user should not expect to see any 
change in behavior of MeV.
**Notes**
1. On Windows and Mac OS X (10.6) where the default JVM is 64 Bit, the 
user will be thrown a warning to change to 32 bit JVM. This is required 
because the API is not ready for 64 Bit environment yet and we are 
working on a solution. However once the default JVM is set to 32 Bit, 
the R dependent modules would run. To help the users setup the 32 bit 
JVM we will be providing help and assistance to do the following:
a. On Windows: To install 32 Bit Java if not already installed and to 
modify the launch script TMEV.sh to point to it.
b. On Mac OS X we would provide instructions on how to set up 32bit JVM 
as default. The default in OS X 10.6 (Snow leopard is 64 bit).
2. On Mac we expect the user to have R 2.9.x universal binary installed 
in the Application Framework. We do not expect such for Windows and 
Linux systems.
3. Please use MeV SourceForge page for submitting queries, questions and 
issues. We have set up a page for this particular JVM issue named R MeV 
Integration, JVM issues.

LIMMA Module
Linear Models for Microarray Data, a statistical framework for the 
analysis of gene expression microarray data, using linear models for 
analyzing designed experiments and the assessment of differential 
expression, was implemented as a new module into MeV.
This module was implemented using the R framework described above and 
without writing a single line of Java code for the numerical analysis.

NMF Module
Non-negative Matrix Factorization, a technique which makes use of an 
algorithm based on decomposition by parts of an extensive data matrix 
into a small number of relevant metagenes, has been implemented as a new 
module into MeV. NMF’s ability to identify expression patterns and make 
class discoveries has been shown to able to have greater robustness over 
popular clustering techniques such as HCL and SOM.

GSEA UI Rewrite
GSEA user interface has undergone a major revamp in this release. The 
slick new UI is more intuitive and user friendly. Two additional viewers 
“Leading Edge Graph” --displaying the subset of genes contributing most 
to the gene set level metric and “Test Statistic Graph” --showing how 
genes within a gene set contribute to the overall gene-set-level metric 
have been also been added.

Nested EASE
Nested EASE (nEASE) is an extension of the EASE module. The nEASE 
algorithm includes a second, sub-level, iterative Fisher’s Exact Test on 
significantly enriched GO terms identified in a first-level EASE 
analysis. This sub-classification approach provides increased 
sensitivity for detecting enriched GO terms and thus affords a deeper 
understanding of possible mechanisms underlying a given condition under 
study.
A tutorial describing how to use the new nested EASE feature is 
available on the MeV website, mev.tm4.org.

Venn Diagrams
A new addition to the Cluster Manager allows users to viewer 
relationships between two or three clusters of samples or genes in the 
form of a Venn Diagram. This interactive addition also displays a 
p-value for two-cluster diagrams representing the likelihood of the 
given overlap occurring in a random sampling of identical size.

Minor Additions
* EASE analysis results now save much more efficiently.
* Most File Choosers now default to the last-used data directory.
* The Gaggle interface now supports metadata as part of its broadcast. 
See the Gaggle page on the MeV website for details.
* Chromosomal location annotation will now be rendered as links to the 
UCSC Genome browser in MeV’s standard table views.
* Expression data can be viewed in the Institute for Systems Biology’s 
Genome Browser, through a new right-click menu option in many result 
viewers. This feature requires that chromosomal location information has 
been loaded.
* Enabled multiple selecting for automatic cluster creation.
Bugfixes
* USC no longer throws an error when a result set of size zero is returned.
* PCA, COA and TRN modules can now save and load analysis results 
regardless of whether Java3D is installed.
* The title bar in error message dialogs read an appropriate “Algorithm 
Exception” instead of “Out of Memory Exception”.
* A bug in EASE prevented the use of the Trim Options checkbox. This has 
been fixed.
* The Save Analysis progress dialog now responds to the Cancel and close 
window buttons.
* The state-saving functions of the SAM and TTEST modules have been 
re-written for greater speed and stability.
* Cluster Manager heatmaps and expression viewers no longer fail when 
clusters are created on data that has been filtered.
* Rank Products no longer misreports p-values for datasets larger than 
40 samples.
* Inverted “Show Color” checkbox in Cluster Manager is fixed.
* Fixed null pointer exception in Original Data viewer when launching 
new session.
* PPI seeding in BN module was not reading the ppi file correctly 
leading to missed interactions. It is now been fixed.
* BN module would not run on Windows if install path had spaces in them 
(e.g. ‘Documents Settings’, ‘Program Files’ etc). This problem has been 
fixed.
* GEO GDS and Series Matrix file loaders have Affymetrix as default 
selection
* Null pointer exception no longer thrown on clicking heat map cells 
after loading GEO files
* MeV file loader loads data even if annotations are missing

Known Issues
* The LIMMA module will not be accessible when MeV is launched via Java 
Webstart. This is due to difficulty with including the required R 
libraries with the Webstart download. We expect to address this problem 
for the next major MeV release in May. Until then, the workaround is to 
download MeV and run it from the local desktop.

Questions? Comments?
Please let us know in the MeV forums.
https://sourceforge.net/forum/?group_id=110558