[BioC] Recent changes to Bioconductor packages

[madman at jimmy.harvard.edu]

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.
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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.