[BioC] Recent changes to Bioconductor packages

madman at jimmy.harvard.edu madman at jimmy.harvard.edu
Sat Aug 30 06:00:02 MEST 2003

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.
August 29, 2003: limma 1.1.13 - reorganization of heatdiagram and classifyTests
    functions.  GKS

August 28, 2003: metaData - three new data packages namely humanLLMappings, 
    mouseLLMappings, and ratLLMappings containing mappings between 
    LocusLink ids to GO, PubMed, and UniGene ids and vice versa were 
    added. JZ

August 28, 2003: metaData - version 1.3.1 was released. JZ

August 28, 2003: AnnBuilder - a bug that cause incorrect mappings to 
    LocusLink id "1" was fixed. JZ

August 28, 2003: limma 1.1.12 - add ArrayVision support to read.maimages.  Many other
    small changes including a backgroundCorrect method to ensure positive
	intensities.  Expansion of sections on reading data in User's Guide.

August 27, 2003: annaffy - A number of changes:
    * Added new search functions aafSearchText() and aafSearchGO() for searching
      metadata. See the vignette for more information and examples.
    * Created new class aafProbe. getURL() method returns a deep link to the
      NetAffx(tm) Analysis Center. Thanks to David Kulp.
    * Fixed a couple small bugs in aafTableFrame() and aafTableInt(). CS

August 25, 2003: Rgraphviz - Edges will now honour lty and lwd parameters JG

August 25, 2003: graph - the edgeWeights() method will now also provide
    node names for the names of the weights vectors in all cases.  Previously,
    if no weights were specified, edgeWeights() generated a vector of
    all 1's, but did not name the vector. JG

August 25, 2003: Rgraphviz - a convenience method weightLabels() was added
    for the graphNEL class which will return edge weights in a format
    appropriate for the 'edgeLabels' parameter to the plot method.  This
    allows users to have the edge weights as labels. JG 

August 21, 2003: Rgraphviz - Edge labels are now implemented. JG

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