[Bioc-devel] NEWS September 2006

[James MacDonald]

	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



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