October Changes in BioC Devel

    October 2006

affycoretools
    Added vennSelectFC() which emulates vennSelect() for those
    cases where there is no replication
   
affyPLM
    Added preprocess() which does normalization and background
    correction only

affyQCReport
    Added affyQAReport(), which will create a pdf containing
    various QA plots for an AffyBatch

AnnBuilder
    Exported resolveMaps() from namespace per user's request
    Fixed bug in YEASTGENENAME that was not correctly reporting the name
   
annotate
    Added filterGOByOntology() helper function that takes a vector
    of GO IDs and returns a logical vector indicating which are in
    the specified ontology (MF, BP, CC)
   
Biobase
    Deprecated exprSet and phenoData classes. Methods with exprSet
    and phenoData in their signature have been deprecated
   
    Updated biocReposList to Bioc 2.0 repositories

    Added lcsuff() to compute the longest common suffix of a set
    of character strings - this will help to shorten the names of
    some things like microarray names

    Added code to make a package from an ExpressionSet

biomaRt
    Fixed exportFASTA() so it works with the data.frame output of
    getSequence()
   
    Enabled use of archived BioMart databases in MySQL mode
   
    Fixed a bug in simple biomaRt functions when used on a local
    BioMart database

BSgenome
    Added the [[ method for BSgenome objects
   
    Added the 'length' method for BSgenome objects

BufferedMatrix
    Made as.BufferedMatrix() do more at the C code level to speed
    things up

    Added colRanges, colMedians
   
    Added filenames(), memory.usage(), disk.usage() methods

Category
    Added DatPkg class to provide abstract interface to annotation
    data

    Use filterGOByOntology() for hyperGTest() - this avoids the
    use of the GOTERM env and should be faster and use less memory

    Added methods to use humanLLMapping as annotation package

    Fixed bug in expected count for hyperGTest()
   
cellHTS
    Changed the output of imageScreen(obj) to integer. Added
    vertical lines to the boxplot and controls plot to separate
    different batches

flowcore
    New Package:
        Provides S4 data structures flow cytometry data.
    Maintainer:
        Nolwenn Le Meur

genefilter
    Fixed bug in pAUC computation

    Fixed bug in rowpAUCs and added class and methods to deal with
    ROC objects. Added generic and methods for rowFtests

GOstats
    Added helpers for GOHyperGResult objects; sigCategories() -
    list GO IDs that are significant, selectedGenes() - list genes
    from selected gene list for given GO ID, plotTermGraphs() -
    plot connected components of significang GO terms

limma
    read.maimages() with dource = "quantarray" now sets annotation
    columns

    Added a namespace to the package. All functions not starting
    with "." are exported

    Changed column header for topTable. M renamed logFC, A renamed
    AveExpr

    lmFit() not supports ExpressionSet objects, volcanoplot() now
    allows NULL for names argument

    New function strsplit2(), which replaces splitName()

macat
    Added warning regarding permutations with small sample sizes

makePlatformDesign
    Fixed bug for NGS parser

    Fixed problem when generating PDEnvs for NGS Tiling arrays

pcaMethods
    Added parameter 'completeObs' to all pca methods, so end users
    can choose if the complete observations should be returned

    Added parameter 'center' to pca methods

    Changed threshold in ppca() to 1e-5, which will lead to more
    stable results

SNPscan
    Added a namespace
   
    Added accessors for snpcopynumberset
   
    Fixed bug in plotSnp

    Added plotChromosome method

    plotSnp() is now a wrapper for plotChromosome(). Updated
    plotCytoband()
   
    Renamed SNPscan --> SNPchip