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.

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. ---------------------------------------------------------------------- - June 13, 2003: Data packages - rae230a, rae230b, mgu74bv2, and mgu74cv2 added. YG replaced by YEAST -JZ June 12, 2003: Biobase - new casting method: as.data.frame.exprSet -- LG June 12, 2003: limma - imported version 1.1.0. New function lmFit. classifyTests fixed. GKS June 11, 2003: limma - imported version 1.0.9 - first version of MArrayLM class. Start on bug fix to classifyTests. GKS June 9, 2003 - AnnBuilder: a bug that causes miss match between ORF ids and gene names was fixed. -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. ---------------------------------------------------------------------- - June 20, 2003: Biobase/reposTools - Converted both packages to use the install.R mechanism for installation. This should result in much faster startup times when loading these packages. JG June 20, 2003: reposTools - fixed a small bug in the splitDFstrings man page which was causing problems on examples in R-devel. JG June 19, 2003: limma - version 1.1.2 - bug fixes to classifyTests, normalizeForPrintorder (no longer generic) and plotPrintorder. ClassifyTests now accepts design and contrast matrices. GKS June 18, 2003: reposTools - added a 'BIOCcdf' repository alias. JG June 18, 2003: getBioC - the default for the getAllDeps parameter is now TRUE. JG June 15, 2003: limma - version 1.1.1 - new functions for Kooperberg Bayesian background correction. modreg now required for R earlier than 1.7.0. normalizeWithinArrays no longer generic to simplify documentation. Documentation for normalizeBetweenArrays also consolidated. New virtual class LargeDataObject and associated show method.

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. ---------------------------------------------------------------------- - 28 June 2003: limma - imported version 1.1.4. New function designMatrix to construct design matrices for microarray experiments with common references. cbind methods for MAList and RGList objects. New function loessFit giving substantial speed improvements for loess normalization. 27 Juna 2003: Data packages version 1.2.7 are available from the web. Tens to over a hundred more genes are annotated than the previous one. JZ. 27 June 2003: tkWidgets - filterMaster added to allow users to perform gene filtering using a widget. JZ. 27 June 2003: annotate - CHRLOC2chromLoc (and by extention buildChromLocation) now allows for genes with multiple mappings. JG 26 June 2003: annotate - Removed the chromLoc class JG 26 June 2003: tkWidgets - converted to use the install.R system JG 26 June 2003: annotate - converted to use the install.R system JG 26 June 2003: DynDoc - converted to use the install.R system JG 26 June 2003: ROC - converted to use the install.R system JG 26 June 2003: Rgraphviz - edited the output of plot to put in the node heights & radius (which for ellipises is really half of the width) JG 25 June 2003: AnnBuilder - GO XML parser modified in response to changes of tag names made by Gene Ontology (part-of to part_of and isa to is_a). JZ 25 June 2003: makePMG - a new packages added. makePMG takes a Bioconductor data package (e. g. hgu95av2) and then makes a new data packages containing graph objects with probe ids, symbols, or LocusLink ids as node ids. Edges connects two nodes that were co-cited by an artical abstracted by NLM. JZ 24 June 2003: Biobase - added function 'package.version' which will report the version # of an installed package. JG 23 June 2003: limma - imported version 1.1.3 - extra arguments added to kooperberg function. Internal kooperberg functions now hidden from user. New affy example added to User's Guide.