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. ---------------------------------------------------------------------- - 05 Feb 2004: reposTools - A bug that was causing packages which failed to install to be registered in the database as an installed package was fixed. JG 05 Feb 2004: getBioC - getBioC will now also check for the minimum required version of R for relLevel of "devel" as well as "release", so that we can check for two tracks of R. JG 05 Feb 2004: Rgraphviz - agopen now will allow a user to manually supply a list of pNode and pEdge objects instead of automatic transformation from a graph object. JG 03 Feb 2004: Rgraphviz - the 'xlab' and 'ylab' parameters now work, and a 'main' parameter was added. JG 03 Feb 2004: impute - new package added to perform imputation for microarray data - JG 03 Feb 2004: simpleaffy - new version checked in. 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. ---------------------------------------------------------------------- - Feb. 11, 2004: widgetTools - A bug that caused incorrect selection of check boxes 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. ---------------------------------------------------------------------- - 21 Feb 2004: limma 1.5.1. - now passes R cmd check for R >= 1.7.1 including R1.9.0dev - removed package argument from calls to .C and .Fortran loess hooks in modreg package. - edited package dependencies in DESCRIPTION file. - dimnames and length methods for RGList, MAList and MArrayLM objects - bug fix in duplicateCorrelation() which was not finding the M matrix when object was not an MArrayLM - new argument 'resort.by' for toptable() and topTable() - changes to loessFit() to avoid errors with small numbers of observations - argument 'path' added to readSpotTypes() and readTargets() - check in duplicateCorrelation() for correlation less than -1 - more expository comments added to 2.Classes.Rd - duplicateCorrelation now uses randomizedBlockFit from the statmod package instead of gls from the nlme package. This results in a several- fold increase in speed for duplicateCorrelation and dupcor.series. - dupcor.series now deprecated - getLayout() now has option to guess spacing between duplicate spots - new function blockDiag() to form block diagonal matrices - fix bug in imageplot() which caused overprinting of plots when using par(mfrow) - new function poolVar to Welch-style pooling of sample variances with unequal variances - new functions usersguideURL() and .First.lib() to implement limma entry in Windows drop-down Vignettes menu - bug fix for write.fit() (was failing when adjust p-values with multiple contrasts) - updates to references as linear modelling paper now accepted for publication

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.