A reminder to Bioconductor users that we will be releasing version 1.2 of Bioconductor on Wednesday, May 28th. Information about this release is available at: http://www.bioconductor.org/relNotices/1.2/relNotice_1.2.html The text of which (sans hyperlinks) is available below: ------------------------------------------------------ Upcoming Bioconductor Release 1.2 On May 28, 2003, there will be a release (version 1.2) of the Bioconductor software. Please check back here over the next few weeks for information as we will be updating this page as needed. Release 1.2 is intended to be operated with R version 1.7.X, which can be obtained at CRAN. What features does this release provide? All packages from the 1.1 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 1.2: affy: The affy package now provides for the automatic downloads of necessary CDF packages. There is also a new function, justRMA() which will use less system resources if one just wants RMA vs. using ReadAffy() and then rma/expresso - this will solve some users' problem when they do not have enough memory for working with the full method. The package's implementation of MAS 5.0 now agrees better with Affymetrix's then in previous releases, and now includes a function mas5() to make it easier for a user to obtain these results. * affycomp: A new package that serves as a graphics toolbox for the assessment of Affymetrix expression measures. * AnnBuilder: DB support is no longer required. ABPkgBuilder now provides a signle API for building of data packages. Also, data packages built with AnnBuilder will include an evidence code and association information for GO ids. * Biobase: The exprs2excel method for the exprSet class has been added, which will create an excel friendly file from the expression component of an exprSet. * DynDoc: A new package that provides a set of functions to create and interact with dynamic documents and vignettes * limma: A new package that provides functionality to handle linear models for microarray data. * makecdfenv: A package to create hash table environments from CDF files, as well as functionality to create data packages out of these environments. * RBGL: A new package that provides an interface to the Boost libraries for graph manipulation. * Rgraphviz: A new package that provides an interface with Graphviz to plot graph objects in R. * Ruuid: A new package that provides Universally Unique ID values (UUIDs). * SAGElyzer: A new package that will store SAGE data in a database and then provide functionality to locate genes that are similar to a given SAGE tag. * tkWidgets: The importWizard functionality was added, which provides an Excel style interface for importing data into R. Also the DPExplorer is new in 1.2 - allowing users to explore a BioC data package. The argsWidget widget set will create a GUI for accepting input dynamically. * vsn: vsn can now be used as a normalization method with the affy package. The likelihood function optimization has been streamlined and is faster. There is a new function to produce a diagnostic plot for the variance-mean relationship of microarray data, meanSdPlot. The data returned by vsn is now an object of class "exprSet". * widgetTools: A new package that provides user friendly tools to create Tcl/Tk widgets in R. Any questions should be directed to Jeff Gentry.