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. ---------------------------------------------------------------------- - 04 March 2004: PROcess: Added new package. JG 04 March 2004: Ruuid - Modified the .Call() calls to meet current standards. JG 04 March 2004: limma 1.5.3. - new function smoothVar() - source="agilent" added to read.maimages - bug fixed in heatdiagram() and heatDiagram() which caused over- printing when using par(mfrow) - vennCounts() now uses table() for major computation and is therefore much faster - new function FStat() - S3 class "classification" replaced by S4 class "TestResults", including 'show' and 'summary' methods - classifyTests(), classifyTestsT() and classifyTestsP() now produce "TestResults" objects 02 March 2004: annotae - getDOdesc modified in response to changes in the GO data pacakge. The argument "which" can be MF, CC, BP, or ANY. JZ 02 March 2004: graph - Added a set of coersion functions & methods to convert various forms of matrices into graphs. An adjacency matrix can be directly converted to a garph using 'as', and the functions 'aM2bpG' and 'ftM2adjM' have been added as well. JG 02 March 2004: EBarrays - Added a new contributed package, EBarrays, which provides tools for the analysis of replicated microarray data across multiple conditions. 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. ---------------------------------------------------------------------- - 12 Mar 2004: limma 1.5.6. GKS - tetragamma() changed to psigamma(x,deriv=2) with R version check - bug fix to normalizeRobustSpline() to prevent error when spline basis becomes singular - La.eigen() to eigen() in is.fullrank() 12 Mar 2004: convert 1.1. GKS New package for converting between microarray data classes. 10 Mar 2004: ecoliLeucine - moved it over to experimental data. JG 10 Mar 2004: experimental data - there is now a reposTools style repository for experimental data. JG 10 Mar 2004: reposTools - added an option to 'repositories2' to automatically detect the BioC experimental data repository. JG 10 Mar 2004: several packages - removed the use of 'multiget' in favor of 'mget'. JG Mra 9, 2003: metaData - New versions of annotation are available for downloading from the seb site. NULL values in the GO environment have been replaced by NA. JZ 8 Mar 2004: limma 1.5.4. GKS Now passes R CMD check in R 1.9.0dev. - new argument 'mar' for vennDiagram(), reduces white-space for venn Diagrams - new argument 'annotation' for read.maimages() - fix bug in gls.series to ensure that spacing and weights arguments are passed to duplicateCorrelation() - check for R version when setting package argument for .C and .Fortran calls

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. ---------------------------------------------------------------------- - 19 Mar 2004: affy 1.4.21 (this reports changes that happened during the very last versions). LG - the pack needs R-1.9.0-to-be-released (a fairly recent R-devel is enough). - the deprecated option 'xy' in indexProbes (and friends) was removed. - the xy coordinates starting at one (but not at zero) complication has been sorted out (package-wide option introduced as a global switch) - fixed issue with computeExprSet when querying unknown affyids (no longer crashes). - better handling or errors when running computeExprSet 17 Mar 2004: altcdfenvs - A package to help building alternative associations between identifiers and probes on microarrays. The code and examples apply directly to Affymetrix data. The vignette provides a step-by-step tutorial to go from a given set of reference sequences in a FASTA file to a cdfenv to be used with AffyBatch objects. LG 16 Mar 2004: limma 1.5.7. GKS - Sweave-style vignette added, as well as User's Guide - new function array2channel() to convert targets files from by-array to by-channel representation - removed warning about Cy3, Cy5 columns from readTargets() - more general use of 'ref' in modelMatrix(), doesn't have to occur on every array - target names are sorted in modelMatrix() - designMatrix() renamed to modelMatrix(), designMatrix() deprecated - new function lmsc.series() for single-channel linear models 15 Mar 2004: Biobase - modified the openVignette code to use the new .rds metafiles instead of the 00Index files. 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.