[TM4-Announce] MultiExperiment Viewer v4.0beta released

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

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The TM4 development team is proud to announce the release of
MultiExperiment Viewer version 4.0 beta.  This is a major update to the
program and includes many new features, such as new file loaders for
Agilent and Affymetrix data formats, comparative genomic hybridization
viewers and analysis algorithms, linear expression maps, and an
uncorrelated shrunken centroids module.

Download the program at http://mev.tm4.org/.  This is a beta release, and
as such is for evaluation purposes only.  See the release notes (below)
and the MeV v4.0b Manual
(http://www.tm4.org/documentation/MeV_Manual_4_0b.pdf) for more details on
the new features.


Thank you for your interest in TM4,
The TM4 Development Team



************ MeV v4.0b Release Notes ****************

MAJOR ADDITIONS

**RAMA: Robust Analysis of MicroArrays (MeV Manual Section 5.2)
RAMA can be found under the Adjust Data -> Replicate Analysis menu.  Use
it for robust estimation of cDNA microarray intensities with
replicates.  The package uses a Bayesian hierarchical model for the robust
estimation.  Outliers are modeled explicitly using a t-distribution, and
the model also addresses classical issues such as design effects,
normalization, transformation, and nonconstant variance.

**Analysis-Saving Rewrite
The analysis-saving functions of MeV have been rewritten and made more
robust for the purposes of transferring saved analyses between
computers.  Most of the changes are 'under the hood' and only of interest
to developers.  However, users should keep in mind a few caveats:  

Because of these the changes to the format of saved analysis files (*.anl
files), MeV 4.0b cannot open saved analysis files created by MeV
3.1.  Furthermore, because MeV 4.0b is a test release, we cannot guarantee
that future versions of MeV will be able to open files saved with
v4.0b.  Rest assured, we will do our best, but if testing of this beta
version of MeV reveals problems with analysis-saving, we will have to
sacrifice backwards-compatibility in this case.  Future versions of MeV
after v4.0final will be able to open analysis (*.anl) files created by MeV
v4.0final and later.  

**New File Loaders
File loaders for a variety of file formats have been added to MeV's 'Load
Data' menu.  Some examples include GEO SOFT and dChip.  See the MeV manual
for more details.  

**CGH Viewer & Analyzer (MeV Manual Section 13)
aCGH or Array Based Comparative Genomic Hybridization uses Cy5
(red) labeled tumor DNA and Cy3 (green) labeled normal DNA to determine
gene copy number increases or losses on spotted cDNA or oligo arrays. The
CGH module of MeV provides functionalities to load, visualize & analyze
such datasets with a rich set of graphical tools & log ratio threshold
based analysis algorithms.  

NEW MODULE DEVELOPMENT

**LEM: Linear Expression Maps (MeV Manual Section 11.20)
The Linear Expression Map module produces an expression viewer which maps
gene expression to chromosomal location.  Navigational aides and
expression graphs allow one to visualize and track the expression of
neighboring loci over the experimental conditions under study.

**TEASE: Tree-EASE (MeV Manual Section 11.2)
TEASE is an improvement to the existing HCL module. Use it to find
over-represented GO-term categories in each branch of a HCL tree.  

**BRIDGE: Bayesian Robust Inference for Differential Gene Expression (MeV
	  Manual Section 11.28)
The package fits a robust Bayesian hierarchical model for testing for
differential expression.  This package is written in the R programming
language and therefore requires access to an RServe server.  See the
Appendix of the MeV manual for instructions in installing R and RServe.

**USC: Uncorrelated Shrunken Centroids (MeV Manual Section 11.29)
USC is an integrated classification and feature selection algorithm
applicable to microarray data with any number of classes.  The algorithm
is motivated by the shrunken centroid (SC) algorithm (Tibshirani et
al. 2002) with the following key modification: USC exploits the
inter-dependence of genes by removing highly correlated genes.


BUG FIXES/MINOR ADDITIONS

.	New Affymetrix-, Bioconductor- and GenePix- specific data filters 
	are available under Adjust Data -> Data Filters.
.	choose File-> Customized Application Menubar to create a new
	MultipleArrayViewer window with only a subset of the available module
	buttons shown.
.	A direct link to the MeV manual is available under Help -> MeV Manual.
.	PubMed references found in Credits->Papers/Publications are now 
	linked to the PubMed repository.
.	Two Factor ANOVA fix to handle possible machine precision rounding
	error.
.	Support Tree (ST) repair to restore selection of distance metric.
.	Template Matching (PTM) repair to handle cases where the cluster 
	manager has clusters from more than one source algorithm.
.	EASE repair to handle European number formatting conventions.
.	EASE updates are now handled more robustly.
.	RN annotation mapping fix: previously, displayed annotation in 
	RNViewer was incorrect if a filter had been applied to the data
	before running RN
.	PTM fix to handle problem when the cluster repository contained 
	clusters from multiple algorithms.  Empty clusters are also
	handled correctly.