The Bioconductor core group would like to announce the 1.3 release of the Bioconductor software. There are many new packages as well as several major upgrades and fixes in older packages, and users are encouraged to check them out. Release 1.3 is intended to be operated with R version 1.8.X, which can be obtained at CRAN (http://cran.r-project.org/) -- WHAT FEATURES DOES THIS RELEASE PROVIDE? All packages from the 1.2 release are included. All current bug fixes have been applied, and most have upgraded and provide enhanced functionality. -- NEW PACKAGES AND MAJOR UPGRADES FOR RELEASE 1.3 -- The following is an overview of the most important changes, additions, and upgrades: --- affy There have been many improvements to the affy package. There were big speed and memory improvement of ReadAffy, read.affybatch, justRMA. A mas5calls method was added to get Affymetrix's P/M/A calls. Cel and Cdf classes are no longer supported. Function, read.celfile and other Cel related methods and functions removed. Most Cdf related functions have moved to the makecdfenv package. Function read.probematrix added. It reads CEL files and returns a matrix of PM, MM, or both. This function is more memory efficient than read.affybatch. Also, affy no longer depends on the affydata package. For this reason some examples have been moved from affy vignettes to the affydata vignette. The previously deprecated express function has been completely removed. Lastly, most normalization routines for AffyBatches can now be called with the parameter type which specifies whether the normalization should be applied as a PM-only, MM-only, both PM and MM together or PM and MM separately. --- affycomp: New assessment was added: assessSpikeIn2. Examples of new feature: Local slopes are computes and ROC curves divided by overall expression. Also, all functions that work for hgu95a spike in now also work for hgu133a spike in experiment --- annaffy: Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria. --- Biobase: The generic function as.data.frame() now works on objects of class exprSet. This lets one access the extensive modeling facilities through formula offered by R and packages like 'nlm'. --- factDesign: A package containing functions useful for analyzing data from factorial designed microarray experiments. --- gpls: Classification using partial least squares (PLS), a popular dimension reduction tool in chemometrics, in the context of generalized linear regression based on a previous approach, Iteratively ReWeighted Partial Least Squares (IRWPLS) by Marx (1996). Both two-group and multi-group classifications are incorporated. Firth's bias reduction procedure is also incorporated to ensure more stable and finite regression coefficients. --- graph, Rgraphviz, and RBGL: Graph/Network handling is greatly improved. There is tighter integration between graph, RBGL and Rgraphviz. Colors and SubGraph layouts are now supported in Rgraphviz. RBGL support includes minimal spanning trees, both strong and weakly connected components, and Dijkstra's shortest path algorithm. In graph, enhancements in validity checking and representation have been made. New classes have been established that will allow for general representations of nodes and edges. Capabilities include adding or deleting both nodes and edges, combining sets of nodes into a single node. Unions, intersections and complements of graphs defined on a common set of nodes. Joining of two graphs into a single graph. Functions to compute indegree and outdegree. --- limma: Substantial updates including support for more image analysis programs, new background correction methods, single channel normalization, support for import of exprSet and marrayNorm data objects, improved support for design and contrast matrices, new fitted model object class, within-gene multiple testing, Venn diagrams and generally a move to a simpler command style at the user level. --- matchprobes: A new package providing tools for working with probe sequence information: calculate ATCG content, reverse, complement, mismatch sequences; fast exact sequence matching; combine AffyBatches of different chip types; create probe data packages. --- Measurement.cor: A package to fit a two-level measurement error model for estimation of correlation coefficient between two random variables assuming bivariate normality for both the true value and measurement error. This model allows dependence between measurement errors hence is more flexible. --- ontoTools: Software for working with ontologies (structured vocabularies) and their associations with general data resources. --- Rdbi, RdbiPgSQL: Generic framework for database access in R. Adapted from Rdbi authored by Timothy H. Keitt, with methods for accessing data stored in PostgreSQL tables (Adapted from Rdbi.PgSQL, authored by Timothy H. Keitt) --- SNPtools: Currently an interface to the SNPper data resource maintained at Childrens' Boston, which curates SNP-related data from a variety of sources. --- splicegear: A new package that works with oligonucleotide microarrays designed to monitor or confirm the existence of splice variants. It can extract simple splice-variant information in XML format. This is demonstrated by the connectivity to an existing database of putative splice variants. The package can also integrate easily with the results obtained from the package 'matchprobes'. --- vsn: Two new functions were added 'sagmbSimulateData' and 'sagmbAssess' to quantitatively verify finite sample properties and outlier robustness of the parameter estimation in vsn(). -- TOOLS: The released packages include tools which facilitate: * annotation (AnnBuilder, annotate). * data management and organization through the use of the S4 class structure (Biobase, marrayClasses, limma). * identification of differentially expressed genes and clustering (edd, genefilter, geneplotter, multtest, ROC, limma) * analysis of Affymetrix expression array data (affy, affycomp, gcrma) * diagnostic plots and normalization for cDNA array data (marrayInput, marrayNorm, marrayPlots) * storage and retrieval of large datasets (rhdf5, externalVector, Rdbi, RdbiPgSQL). * facilitate user interaction (tkWidgets, widgetTools) There are currently a total of 48 packages, not including precomputed annotation data packages for Affymetrix GeneChips(tm), KEGG, GO, and LocusLink mappings. -- HELP AND RESOURCES: The packages and more details may be found on the Bioconductor WWW site: http://www.bioconductor.org/ Information on subscribing to the mailing list and viewing its archives can be found at: http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Please use that list to discuss Bioconductor specific issues, bugs, and problems. Note that every package has a vignette (a literate program which provides an annotated example of the package's use) as well as possibly some "HOWTO"s. These document the tool's usage, and are provided in the "doc" subdirectory of each package library. -- WHO: For the Bioconductor development team: Douglas Bates, University of Wisconsin, USA. Ben Bolstad, Division of Biostatistics, UC Berkeley, USA. Vince Carey, Harvard Medical School, USA. Marcel Dettling, Federal Inst. Technology, Switzerland. Sandrine Dudoit, Division of Biostatistics, UC Berkeley, USA. Byron Ellis, Harvard Department of Statistics, USA. Laurent Gautier, Technial University of Denmark, Denmark. Robert Gentleman, Harvard Medical School, USA. Jeff Gentry, Dana-Farber Cancer Institute, USA. Kurt Hornik, Technische Universitat Wien, Austria. Torsten Hothorn, Institut fuer Medizininformatik, Biometrie und Epidemiologie, Germany. Wolfgang Huber, DKFZ Heidelberg, Molecular Genome Analysis, Germany. Stefano Iacus, Italy Rafael Irizarry, Department of Biostatistics (JHU), USA. Friedrich Leisch, Technische Universitat Wien, Austria. Martin Maechler, Federal Inst. Technology, Switzerland. Colin Smith, Scripps Research Institute, USA. Gordon Smyth, Walter and Eliza Hall Institute, Australia. Anthony Rossini, University of Washington and the Fred Hutchinson Cancer Research Center, USA. Gunther Sawitzki, Institute fur Angewandte Mathematik, Germany. Luke Tierney, University of Iowa, USA. Jean Yee Hwa Yang, University of California, San Francisco, USA. Jianhua (John) Zhang, Dana-Farber Cancer Institute, USA. -- rossini@u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}