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 2004: limma 1.7.0. GKS All the linear modelling functions now pass the covariance matrix of the estimated coefficients. This improves support for models with covariance structures: random effects models for technical replicates, mixed models for log-intensity analysis of two color data, duplicate spots etc. Lots of updates to help files. pdf of User's Guide updated. Reading of GPR headers now supported.

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. ---------------------------------------------------------------------- - 16 July 2004: Rgraphviz - Changed the API for custom drawing functions to now have 4 parameters (from 3). The last argument is now 'radConv' and is used to calculate any conversion from Graphviz units to R plotting units (by dividing 'radius / radConv'). JG 12 July 2004: annotate 1.4.7 JWM ll.htmlpage deprecated and replaced with htmlpage, along with new getQuery4XX functions. This allows multiple columns of html links, multiple links per cell, and some checking to minimize busted links. 3 July 2004: limma 1.7.3. GKS plotMA() now accepts exprSet objects to produce between-array MA- plots. Bug fix to imagene file reading.

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 July 2004: affy - 1.5.5 - split.AffyBatch was removed since the split defined for 'exprSet' works now fine (fix by Robert Gentleman). Try 'split(myaffybatch, myfactorormyvector)'. - fix of a bug in plot.ProbeSet (reported, together with the fix by Chang, Kai-Ming, thanks) -- LG 25 July 2004: affy - 1.5.4 - The XY coordinates for probes now starts at 0 (zero) by default. Compatibility with the previous XY coordinates system (starting at one) is made available through the package option 'xy.offset' -- LG