This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 06 September 2003: limma 1.1.17 - new backgroundCorrect options. GKS 04 September 2004: affy - now depends on R 1.8.0 because of new install mechanism. CS 04 September 2003: annaffy - package updated to use the install.R mechanism. CS 04 September 2003: limma 1.1.16 - new argument 'include' in vennCounts and vennDiagram. Support for correlated design matrices added to 'contrasts.fit'. GKS 03 September 2004: annaffy - updated .Rd files to use new R 1.8.0 \alias{} format for S4 methods. CS 03 September 2003: genefilter - Converted to use install.R mechanism. JG 03 September 2003: affy - Affy package was updated to use the install.R mechanism. JG 03 September 2003: limma 1.1.15 - new class exprSet2. new function topTable. New argument 'bin' in loessFit. Fine tuning of interpolation settings used by loessFit. Corresponding changes to documentation. GKS 02 September 2003: Rgraphviz - removed the agset() function and tied the attribute setting to be more directly integrated with agopen() in the C code. JG 02 September 2003: graph - change to edgeWeights() such that weights vectors are now always named. JG 02 September 2003: Imported limma 1.1.14 - read.maimages now supports SMD data files. GKS

This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 12 September 2003: rhdf5 - Due to conflicts with 1.6.X and later of the HDF5 libraries, for now rhdf5 will require that the user has version 1.4.X of the HDF5 libraries through a call in the configure script. JG 11 September 2003: affy - the express function has been formally removed (previously it was marked deprecated). ReadAffy() now calls read.affybatch2() (which should be faster and have a lower memory overhead). justRMA() now calls just.rma2() (which should also be slightly faster and have a lower memory overhead). BMB 10 September 2003: reposTools - when reposTools encounters a library which it can not write to during syncLocalLibList(), it will store the appropriate locLibList structure to a temporary directory which will then be searched (by default) by the other functions such as install/update.packages2() when they are searching for installed versions of packages. Previously if a directory was not writeable then those packages were "dead" to reposTools when the only caveat should be that packages can't be installed there. JG 10 September 2003: reposTools - fixed a major bug with the way in which reposTools selects packages to download. Previously reposTools would always select the first available pacakge from a repository if there were multiple versions of the same package (which always the lowest version number) despite this being the opposite behaviour desired, due to a logic flaw in the way it constructed the package listings for repositories. Likewise, some surrounding code was changed to account for this as the structure itself was 'broken'. JG 09 September 2003: widgetTools - widgetTools now uses install.R JG 09 September 2003: limma 1.1.18 - new function plotDensities and new section in User's Guide on single channel normalization, both by Natalie Thorne. GKS

This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 20 Sep 2003: limma 1.2.4 - ensure that limma passes rcmd check for R 1.8.0 - fix bug in toptable which affected the displayed A-values - new option 'none' for method argument of backgroundCorrect() - new argument 'mar' for imageplot(). GKS 18 Sep 2003: factDesign - A new package providing tools for analyzing data from factorial designed microarray experiments by Denise Scholtens was added. JG 18 Sep 2003: graph - now uses the install.R mechanism JG 17 Sep 2003: gpls - A new package for multi-group classification using generalized partial least squares by Beiying Ding was included in developmental packages. JZ 17 Sep 2003: MeasurementError.cor - A new package for correlation estimation based on two-stage measurement error model by Beiying Ding was included in developmental packages. JZ 16 Sep 2003: reposTools - genRepos() will now handle tarballs with a .tgz extension (as opposed to just '.tar.gz'). JG 16 Sep 2003: vsn - 1. provides two new methods 'sagmbSimulateData' and 'sagmbAssess' that allow to verify and assess how well vsn estimates the calibration and variance stabilization transformations for data that is in fact distributed according to the two-component model with affine array effects (see the SAGMB paper and the vignette.) 2. better control over the least trimmed sum of squares iterative algorithm in the function vsn through the parameter 'cvg.check' (thanks to a suggestion by David Kreil). WH 15 Sep 2003 - added package MAGEML JG 15 Sep 2003 - limma 1.2.0 - fix bug in quantarray read; classifyTests now returns F-statistic. GKS 13 Sep 2003 - SNPtools -- now at version 0.5, stripped down, focusing on bindings to XML-RPC facilities of SNPper snpper.chip.org) -- this will go to 1.0 before the next release. VJC

This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 27 Sep 2003: limma 1.2.5 - changes to read.maimages for ArrayVision data - bug fix for wtIgnore.Filter with GenePix data - new argument 'ties' for normalizeBetweenArrays. GKS Sept. 26, 2003: SAGElyzer - Major interface modification to simplify use. JZ Sept. 26, 2003: widgetTools - dropdownList was added to mimic the behavior of a dropdown list without having to use tcltk extensions. JZ. Sept. 24, 2003: widgetTools - tooltips was added to add tooltip capability for widgets. JZ