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. ---------------------------------------------------------------------- - 30 Dec 2003: limma 1.5.0. GKS - bug fix for designMatrix() (was giving wrong matrix when common reference was Cy5 for first array) - bug fix to printorder() with spacing="topbottom" (was returning vectors of wrong length) - new function modifyWeights() - designMatrix() now uses zapsmall() to eliminate small non-zero entries - readGAL() now sorts GAL files into standard order if they are not already - read.maimages() function now sets the genelist directly from the gpr files, so readGAL() will usually no longer be required - new function auROC() to compute exact area under ROC 27 Dec 2003: Rintact 0.0.0 VJC added package that will derive protein interaction graphs and metadata from EBI Intact project; their web services descriptions are too weak at the moment to make much progress, but browser-derived example XML can be parsed using handlers in this package, and the MIF (molecular interaction format) XML schema is included in inst/MIFXML 27 Dec 2003: NARdbs 0.0.0 VJC added package that contains URLs and descriptions for ~550 databases cataloged in the annual overview of molecular biology databases published in Nucleic Acids Research. Vignette available.

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. ---------------------------------------------------------------------- - 09 Jan 2004 - reposTools - Major changes were made to reposTools (version 1.3.12 is the first to include these), although most of them are "under the hood". The most visible change to users is that the install.packages2() function will now always download the requested packages even if that package is already installed and up to date. Previously this would not happen. JG 09 Jan 2004 - getBioC - getBioC was modified to work appropriately with the new devel version of reposTools (version >= 1.3.12). Users who are tracking BioC-1.3 or have a devel version of reposTools < 1.3.12 should not be affected. JG vsn (04 Jan 2004) - Two major new features: Stratification: vsn can now estimate different calibrations for different groups of probes on an array (e.g. print tip groups, or groups defined by physico-chemical sequence properties) Speed: Through implementing the core code in C and other optimizations, vsn is now faster by about a factor of 15. These improvements are based on contributions from Markus Ruschhaupt and Dennis Kostka. (WH) affy (08 Jan 2004) new function ppsetApply to apply a function over the ProbeSets in an AffyBatch (example with probe-wise t-test in the help file). (LG)

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 Jan 2003 - affyPLM 1.1.0 BMB many major changes including: PLMset-class has new attributes: residuals, varcov image() on a PLMset can now plot residuals and possible to add legend bars. Some major changes in how parameters are passed in some of the C code routines in the fitPLM process conversion function pset2eset() which converts a PLMset to an exprSet rmaPLM() function lets you fit the rma model as a PLMset. weights/residuals allow you to index probes from specific probesets

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. ---------------------------------------------------------------------- - Jan. 23, 2004. MetaData - New versions of annoatation data packages are released. hgu133plus2 were added to the colletion. New features: a) the GO environment is a list of lists with each sublist containing three element namely GOID, Evidence, and Ontology, b) the GO package has two new environment named GOGO2LL and GOLL2GO with mappings between the two ids, c) the KEGG package has two new environments named KEGGEXTID2PATH and KEGGPATHID2EXTID with EXTID being locusLink ids for human, mouse, and rat and ORF ids for yeast. JZ Jan. 23, 2004. AnnBuilder - Code modified to implement the changes in annotation data packages. JZ

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. ---------------------------------------------------------------------- - Jan 30 2004: Rgraphviz - added the ability to lay out the graph using rectangular shapes ("box", "rect" & "rectangle"), and also to draw the nodes with arbitrary drawing functions. JG Jan 30 2004: geneplotter - added the function 'plotExpressionGraph' which can be used to color nodes on a plotted graph by expression levels. JG Jan 30 2004: graph - Added a data set 'integrinMediatedCellAdhesion', providing a graph & related information to a KEGG pathway graph. JG Jan 26 2004: RBGL - C-level bulletproofing added, vignette now completing (VC)