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. ---------------------------------------------------------------------- - 6 Dec 2003: limma 1.3.6 - fix to readSpotTypes() to read column names as.is - new ... argument for readSpotTypes() - rbind method for RGList objects - bug fix for designMatrix(). GKS 1 Dec 2003: limma 1.3.5 - designMatrix() now has new arguments and now handles direct designs - new function write.fit() for outputing results of linear model fit. GKS 2 Dec 2003: genefilter - changed the criteria for success in kOverA and pOverA as per a bug report 3 Dec 2003: biclust - began importing code for the biclust package. I am starting with Cheng-Church and moving on to other ANOVA-based methods. Currently there is refactoring and fixing FLOC bugs. BCE 5 Dec 2003: webbioc Fixed problem with using lower rejection region for t-tests. CS

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. ---------------------------------------------------------------------- - 7 Dec 2003: limma 1.3.7. rbind method for MAList objects. GKS 6 Dec 2003: exprDB - updated configure script for BerkeleyDB 4.2. - now passes CHECK under R-devel by removing dependecy on serialize which is now built-in and checking for "serialize" in .First.lib for older installations. BCE

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. ---------------------------------------------------------------------- - 13 Dec 2003: limma 1.3.8. GKS - bug fix to backGroundCorrect(method="edwards") - bug fix to plotPrintTipLoess() - refinements to estimation of var.prior in ebayes and related functions - coerce (setAs) method for RGList to exprSet2

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. ---------------------------------------------------------------------- - 21 Dec 2003: graph 1.2.2. LG new function 'write.tlp()' to save graphs in the Tulip software file format. 21 Dec 2003: affypdnn 0.3-1. LG Recent bug in expression value computations (following a round of optimization, it was returning all NAs). Fixed 20 Dec 2003: limma 1.3.9. GKS - new function getSpacing() - upgrades to printorder() to accommodate spacing by rows or topbottom - corrections and updates to try to pass R CMD check in R1090dev, but cannot get around that package nlme seems to be broken. 22 Dec 2003: ontoTools 1.2.1 VJC - namedSparse class revised to reduce indirections -- indexing environments jettisoned for simpler vector-based calculations - data elements updated to include version tag, using GO 1.4 - examples/ontoTools vignette updated to work with new data elements - ontoToolsArchiving.Rnw vignette added to illustrate how stored access mats, concept probabilities are computed