From tm4-announce at tm4.org Fri Jul 2 11:44:22 2010 From: tm4-announce at tm4.org (Announcements for the TM4 Microarray Software Suite (http://www.tm4.org/)) Date: Fri, 02 Jul 2010 13:44:22 -0400 Subject: [TM4-Announce] MeV v4.6 is released Message-ID: <4C2E2576.9010108@jimmy.harvard.edu> The MeV Development team is proud to announce the release of MeV v4.6. This is a large update that includes many new features, including several new modules and large improvements to existing favorites.You can download MeV v4.6 at http://mev.tm4.org/ . *Major additions* *Attract Module* The Attract algorithm identifies the core gene expression modules that are differentially activated between cell types or different sample groups, and elucidates the set of expression profiles which describe the range of transcriptional behavior within each module. *Global Ancova Module* A technique for identifying differentially expressed gene sets based off of the calculation of an F-test between groups of samples. Analyses are typically run in a two-class format but may also be applied to additional groups. Global Ancova fits linear models to the data and compares them using the extra sum of squares principle. The result table includes p-values, permutation p-values and asymptotic p-values. ** *Minet Module* For a given dataset, minet infers the network in two steps. First, the mutual information between all pairs of variables in dataset is computed according to the estimator argument. Then the algorithm given by method considers the estimated mutual information in order to build the network. *SURV Module* The Survival (SURV) module contains two functions for the analysis of censored survival data. The first is a basic comparison of the survival curves of two groups of samples. The second feature of the module is the creation of a _cox_ proportional hazards model based on the loaded gene expression data, using survival time as the reporting value. * * *EASE UI Rewrite * The EASE UI is simpler and easier to use now. *Updates to the BN module* /Network Seed/ allows the user is to provide a file representing a network. Network seed can be used in one of the three ways: 1. Using the user network seed alone and bypassing literature based network seeding altogether. 2. Using the user network seed along with Literature mining seed. 3. User provided network is used as a complete network and the network structure is not learned, only the Conditional Probability Tables (CPTs) associated with the network is learned for downstream exploration. A node by the name of "CLASS" shows up in the network which captures the effect of sample groups on the network. Once the network is displayed the "CLASS" node behaves and can be treated as any other node in the network. *Updates to the GSEA module* Two new viewers are now provided, including a p-value graph viewer and a gene set membership plot. Gene sets can now be automatically downloaded from GeneSigDB and MSigDb. *Updates to the SAM module* A new addition to the SAM module integrates RHook to make a newer version of SAM available to users. MeV's SAM now makes use of serially correlated time-course data in the exploration of statistically significant gene expression. *Hierarchical Clustering Trees* MeV now displays hierarchical trees with meaningful and proportional node heights along with an optional scale tailored to the chosen distance metric used in constructing the tree. *Other Changes* Rama significance testing for spotted array data has been disabled, along with the Bridge module. These functions never worked properly and have been unsupported for some time. They are still available in older versions of MeV. The most recent version of MeV that contains these features is MeV v4.5.1 . We have also retired the Single Array Viewer. *Minor Additions* * FDR calculation is displayed in the TTEST module. * Annotation can now be auto-loaded by MeV after expression data has already been loaded. * Agilent file loader has been updated to work with the latest file formats. * Pearson correlation coefficients are now the default distance metric for most analysis modules. *Known Issues* * MeV's R-driven modules (LIMMA, Attract, Surv, SAM, etc) 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. Until we identify a solution to this problem, the workaround is to download MeV and run it locally. *Questions? Comments? * Please let us know in the MeV forums. https://sourceforge.net/forum/?group_id=110558 ** -------------- next part -------------- An HTML attachment was scrubbed... URL: