September Changes in BioC Devel

    September 2006

ABarray
    Combined doPlotEset, doPlotFCT, doANOVA, doLPE and doVennDiagram vignettes into ABarray vignette
    Removed knn imputation functionality
    Changed the process for normalization. The default is still quantile, but data analysis can now be performed using different normalizations
   
affxparser
    Added trial version of writeCdf(), convertCdf(), createCel() and updateCelUnits
    Added compareCdfs() which compares CDFs in a memory efficient way and reports differences
    Added a help section for convertCdf()
    Added applyCdfBlocks() to complement applyCdfGroups()
    Bugfix writeCdf() swapped ncols and nrows in CDF header
   
affycoretools
    Added ability to output text files when using the biomaRt related functions
    Updates to plotPCA(), added two arguments pch and col to control the plotting symbols and colors
   

affylmGUI
    Added 'One Slide' and 'All Slides' to many plot options
    Added the 'Intensity Density Plot(All slides)' option
    Added 'RNA Digestion Plot (All Slides)' option
    Added 'NUSE-Normalized Unscaled Standard Errors Plot' option
    Added 'RLE-Relative Log Expression Plot' option
    Renamed the image quality plot on the plot menu to 'Weights pseudo chip Image (One slide) Plot'
   

AnnBuilder
    Changed xxxLOCUSID to xxxENTREZID
    Set LazyLoading as default for all builder functions
    Bugfix: when the probe ids are all numeric, some environments got messed up with probe ids being converted to strings with extraneous spaces at the beginning'
   
annotate
    Moved GOusage vignette and GO helper functions from GOstats to annotate
    Added chrCats() and other functions from iSNetwork
   
beadarray
    Removed obsolete data objects and added more interesting example
    Updated vignettes to describe new ExpressionSetIllumina objects
    Added method for calculating Illumina differential expression statistic
    Added S4 methods and documentation
   

Biobase
    Improved 'combine' method for data.frame and AnnotatedDateFrame
    Internal clarification of VersionedClass initialization
    Added slot 'featureData and accessors featureData and featureData<- to eSet
    Added generic annotatedDataFrameFrom as a convenience for constructing AnnotatedDateFrames
    Improved updateobject, attempting to handle old-style S4 objects extending vector
    [[ and [[<- for eSet, accessing corresponding phenoData slots
    Added platform, gui, interactive checks to addVigs2WinMenu. This patch allows other packages to use a simplified idiom for attaching vignettes to the Windows GUI menu; supressWarnings(require("Biobase")) && addVigs2WinMenu("somePkg") in the .onAttach function
    Encreased speed and decreased screen real estate of show for eSet objects
    Added code and templates for the creation of data packages from ExpressionSets
   
Biostrings
    Added the 'AAString' class (the third direct 'BString' derivation after 'DNAString' and 'AAString') for efficient storage of a sequence of amino acids
    Cleaning and fixes required by new AAString class.
        Cleaned logic and code of the 'initialize' methods for BString and derived objects, added 'copy.data' and 'verbose' args
        Cleaned logic and code of the '==' and '!=' methods for BString and derived objects
    Added the DNA_ALPHABET and RNA_ALPHABET constants and the 'alphabet' method for DNAString and RNAString objects (still missing for AAString objects)
    Added the IUPAC_CODE_MAP, AMINO_ACID_CODE, GENETIC_CODE and AA_ALPHABET constants and the 'alphabet' method for AAString objects
   
Category
    Moved GOHyperG back to GOstats
    Renamed slots pvalue.cutoff => pvalueCutoff, test.direction => testDirection   
    Major rename of classes GeneCategoryHyperGeoTestParams => HyperGParams and similar
    Rename geneCategoryHyperGeoTest => hyperGTest
    Added accessor methods for HyperGParams class
    Added conditional methods for hypergeometric calculation
    Added PFAM methods; thanks to T. Chiang for the patch
    Added code for testing of over and under represention in hyperGTest
   
cellHTS
    Added function to perform B score normalization, and for plotting the spatial effects