Greetings! The Bioconductor core group would like to announce the 5th release of Bioconductor, version 1.4. There are many new packages as well as several major upgrades and fixes in older packages, and users are encouraged to upgrade existing tools and check out the new packages. Release 1.4 is intended to be operated with R version 1.9.x, which can be obtained at CRAN (http://cran.r-project.org/) WHAT FEATURES DOES THIS RELEASE PROVIDE? ======================================== All packages from the 1.3 release are included. All current bug fixes have been applied, and most have upgraded and provide enhanced functionality. SOME OF THE MAJOR UPGRADES FOR RELEASE 1.4: =========================================== -- Proteomics (PROcess, gpls, apComplex) -- Array CGH (DNAcopy, aCGH) -- Cell cycle analysis (GeneTS) -- Packages for lab assay analysis and management (prada) -- Agilent arrays handling in limma -- Annotation tools (Resourcer, GOstat, goTools, ontoTools) -- Improved interfaces (limmaGUI, affylmGUI, webbioc, -- MAGE file processing (RMAGEML) -- affymetrix processing: many improvements, gcrma, affypdnn (probe-dependent nearest neighbors), affyPLM (probe-level models). -- marray (next generation of the depreciated marrayClasses, marrayNorm, marrayPlots, marrayTools packages) -- General analysis tools (rama, qvalue, pickgene, EBarrays, impute, pamr, bim, ) -- QA/QC (arrayMagic, arrayQuality, LPE) -- sequence analysis (pairseqsim, Biostrings) -- interface to the GeneSpring data analysis program (GeneSpring) TOOLS: ====== The released packages include tools which facilitate: * annotation * data management and organization through the use of the S4 class structure * identification of differentially expressed genes and clustering * quality assurance and control * analysis of Affymetrix expression array data * diagnostic plots and normalization for cDNA array data * storage and retrieval of large datasets * user interaction widgets * sequence analysis * proteomics There are currently 81 packages, not including precomputed annotation data packages for Affymetrix GeneChips(tm) and prepackaged general annotation databases such as KEGG, GO, and LocusLink. 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. Try: library(tkWidgets) vExplorer() for assistance after installing BioConductor. 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. A.J. Rossini, Medical Eduction and Biomedical Informatics, University of Washington and Biostatistics, 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. With special thanks to many contributors from around the world. best, -tony -- 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}}

> The Bioconductor core group would like to announce the 5th release of > Bioconductor, version 1.4. Small addendum: please also note two new features of package vsn: - Much faster, due to implementation in C - Possibility of stratification within array (e.g. for print-tip or plate effects) Best wishes Wolfgang ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber