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. ---------------------------------------------------------------------- - July 30, 2003 - Metadata: a new annotation data package -homology was added to the link to metadata. The package containes data for pairwise best matches for different organisms. JZ July 25, 2003 - AnnBuilder: a new function homoPkgBuilder was added to build a homology data package using the homology data provided by NCBI. 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. ---------------------------------------------------------------------- - 07 August 2003: metadata - version 1.3.0 of metadata was released. A new environment HGID was added to packages for all the chips to map probe ids to HomoloGene ids. HomoloGene ids can then be used for mapping to other homology data contained in the homology data package. Note that the licensing for KEGG has been chenged. The KEGG package is free for academic use but requires a license agreement with KEGG for non-academic use. JZ 04 August 2003: limma version 1.1.9 - bug fix to loessFit. Gradually introducing object orientated versions eBayes of ebayes, topTable of toptable, heatDiagram of heatdiagram.

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. ---------------------------------------------------------------------- - 15 Aug 2003: splicegear - fixed bits and added (still undocumented) plot methods using 'grid'. LG 15 Aug 2003: limma 1.1.11 - added functionality to read Imagene data to read.maimages. GKS 14 Aug 2003: MetaData - A contributed CDF package, hgu133atagcdf, was added. JG 11 Aug 2003: Rgraphviz - changed the API to the 'plot' method. Graphviz attributes are now passed in via the 'attrs' parameter instead of piece by piece via separate parameters (and thus now allows for more options). Not all attributes will have a visible effect. More information is available at help("plot.graph"). JG 11 Aug 2003: reposTools - Updated spots of the code to work with changes in the current R-devel. JG

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. ---------------------------------------------------------------------- - August 21, 2003: AnnBuilder - New function, map2LL, that creates a data package with mappings between LocusLink ids to GO, RefSeq, and UniGene ids and vice versa and, chrLocPkgBuilder, that creates a data package with mappings between LocusLink ids and chromosomal locations were added. JZ August 20, 2003: annotate - a new function findNeighbors was added to allow users to find genes neighboring a given gene or genes within a region on a chromosome using CHRLOC data packages. JZ August 20, 2003: MetaData - three new data packages namely humanCHRLOC, mouseCHRLOC, and ratCHRLOC were added. The packages contain chromosomal location data that can be used to locate genes within a given region of a chromosome or genes neighboring a given target gene. JZ August 20, 2003: Rgraphviz - Fixed a bug where node colours were not being honoured in the plotting routine when ellipse shape was specified. JG August 20, 2003: daMA - new package added. JG

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. ---------------------------------------------------------------------- - August 29, 2003: limma 1.1.13 - reorganization of heatdiagram and classifyTests functions. GKS August 28, 2003: metaData - three new data packages namely humanLLMappings, mouseLLMappings, and ratLLMappings containing mappings between LocusLink ids to GO, PubMed, and UniGene ids and vice versa were added. JZ August 28, 2003: metaData - version 1.3.1 was released. JZ August 28, 2003: AnnBuilder - a bug that cause incorrect mappings to LocusLink id "1" was fixed. JZ August 28, 2003: limma 1.1.12 - add ArrayVision support to read.maimages. Many other small changes including a backgroundCorrect method to ensure positive intensities. Expansion of sections on reading data in User's Guide. August 27, 2003: annaffy - A number of changes: * Added new search functions aafSearchText() and aafSearchGO() for searching metadata. See the vignette for more information and examples. * Created new class aafProbe. getURL() method returns a deep link to the NetAffx(tm) Analysis Center. Thanks to David Kulp. * Fixed a couple small bugs in aafTableFrame() and aafTableInt(). CS August 25, 2003: Rgraphviz - Edges will now honour lty and lwd parameters JG August 25, 2003: graph - the edgeWeights() method will now also provide node names for the names of the weights vectors in all cases. Previously, if no weights were specified, edgeWeights() generated a vector of all 1's, but did not name the vector. JG August 25, 2003: Rgraphviz - a convenience method weightLabels() was added for the graphNEL class which will return edge weights in a format appropriate for the 'edgeLabels' parameter to the plot method. This allows users to have the edge weights as labels. JG August 21, 2003: Rgraphviz - Edge labels are now implemented. JG