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MeV v4.4.1 is released
The latest bugfix release of MeV, v4.4.1, is now available for download at http://www.tm4.org. This release contains several small bug fixes. The MeV team recommends that all MeV users upgrade to this newest version.• State-saving optimizations in the TTEST and SAM modules. • Fixed problem in Rank Products analysis that prevented two-class unpaired from running more than 40 samples.• Fixed GUI issues with Cluster Manager.• Changed display of node heights for Hierarchical Clustering.• Fixed cluster storing dialog box bug- dialog box could not be cancelled.• When launched via Java Webstart, MeV now loads data with correct row indexing• Table links to external GO databases now support multiple terms.• Chromosomal location end-coordinates are now loaded fully, rather than with a truncated last digit• Annotation fields are now re-loaded in the same order they were saved in.• Hypergeometrc distribution is now calculated correctly.The TM4 Group
2009-07-01 18:22:48 UTC by dschlauch
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Request for Letters of Support
The grant that funds MeV development is up for renewal and we are seeking letters of support from users of the application. Please consider adapting our draft letter to indicate your support of MeV and help us continue development on a free, open-source Bioinformatics tool.
http://www.tm4.org/mev/request_for_letters.html
2009-06-09 20:37:23 UTC by eleanorahowe
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MeV v4.4 Released
The MeV development team is proud to announce the release of MeV v4.4. 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://sourceforge.net/forum/?group_id=110558Please 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_3dMeV v4.4 releaseMay 28, 2009Major additionsBN Predict Cytoscape Plugin as MeV ExtensionAs an extension to the already published BN method, we have developed a Cytoscape plug-in that does predictive modeling of the BN described above. For each network loaded with an associated conditional probability table (CPT), the plugin calculates probabilities of expression (bin/state probabilities) for each network node. Documentation can be found at http://www.tm4.org/BnPredictMAGE-TAB File LoaderThe MeV MAGE-TAB file loader allows a user to select and load expression data from MAGE-TAB (version 1.0) formatted files. The MAGE-TAB specification can be found at http://www.mged.org/mage-tab/spec1.0.html. This format includes files that describe an experimental series, the samples used in the experimental series, optionally the array design of the microarray chips employed in the study, and a data matrix file containing gene expression data values. New Cluster Manager ToolThe new Cluster Manager allows users to create, visualize, and manipulate clusters and includes numerous new features and enhancements to the previously existing clustering system. RP Two-Class Unpaired and Two-Class Paired experimental designs.MeV now supports the use of the Rank Products module for two-class experimental designs. Previously, only one-class functionality existed for this method. As with most other modules, the Cluster Selector feature is compatible with this addition.Automated Linking to Online DatabasesMeV can now automatically link to online databases, such as NCBI, AmiGO and others. When gene annotation is loaded using MeV's new annotation file loader (under the "annotation" subsection of the file loader) links will automatically be generated from some of these annotations to the appropriate online resource. The specific resources used can be customized for individual users, and expanded to other annotation types not loaded by the MeV automated annotation loader. See the MeV manual for more details. Annotation Support for New ArraysThe MeV team has developed a new tool for creating the annotation files everyone depends on for their data analysis. We will be providing support for many new arrays in the future. These arrays will be available from the ftp site as well as via direct download from within MeV's file loaders. We have also generated new EASE datafiles that provide better, more complete EASE results. Java WebStart ImprovementsMeV can now accept a wider range of command-line arguments, improving its usefulness as a webstarted application. Instructions for getting started with webstart are available at http://www.tm4.org/mev_webstart.html Assignment File Saving Synchronization MeV's assignment file system has been synchronized between virtually all modules and experimental designs. Files saved in each module are compatible with the loaders of other modules. Additionally, the files themselves are saved in a human-readable format that can be opened, read and edited by users. See the MeV manual for more information.Minor Additions* The entire dataset is now displayed in each of the standard viewers - heatmap, expression graph, centroid and table view - immediately upon loading.* New Proportional branch length feature added to Hierarchical Clustering.* A new p-value viewer has been added to GSEA.* Node rotation feature added to Hierarchical Clustering.* Sample reordering feature added to heatmap viewers.* Five standard viewers added to ?Original Data? immediately after data is loaded.* Cluster Selection feature added to SAM module for "One-Class", "Two-class unpaired", and "Multi-class".* New feature allowing multiple clustering by binning.* A new interface to the annotation downloader makes annotation loading easier.* Excel-style copying of data from result tables is now available.* Behind-the-scenes work on state-saving makes it much faster and more robust.Bugfixes* Fixed missing columns in One-Condition BETR output.* Improved handling of missing data in BETR analysis.* Tweaks to make MeV behave better without an internet connection.* SAM no longer tags genes with zero variance as "Negative Significant".Known Issues* Results returned by the RP module in two-class unpaired analysis can become uninformative for datasets with greater than about 40 samples. When the number of samples is too high, the module will report RP values of zero for many of the genes. We recommend using the SAM module instead of RP for these datasets, as RP was designed to work best with small numbers of samples. We plan to have this issue addressed for the next MeV release. Questions? Comments? Please let us know in the MeV forums.https://sourceforge.net/forum/?group_id=110558
2009-06-02 16:41:29 UTC by eleanorahowe
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MeV v4.3.02 Released
The latest bugfix release of MeV, v4.3.02, is now available for download at http://www.tm4.org. This release contains several small bug fixes. The MeV team recommends that all MeV users upgrade to this newest version.Bug fixes:* ResourceManager downloads via HTTP now have a more reasonable timeout setting.* The ResourceManager will now download files provided by servlets.* The EASE initialization dialog box would not initialize when custom annotation files were loaded.* The color-coding of result nodes in TEASE were not set properly.* Tav file loader was not loading preferences files. This has been fixed.* Launching new session from a cluster bug repaired.The TM4 Team
2009-02-05 22:26:58 UTC by eleanorahowe
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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.
2008-12-08 17:14:28 UTC by eleanorahowe
