[Bioc-devel] NEWS September 2006

James MacDonald jmacdon at med.umich.edu
Thu Oct 5 17:41:58 CEST 2006

	September 2006

	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
	Added trial version of writeCdf(), convertCdf(), createCel() and
	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
	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

	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'

	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'
	Moved GOusage vignette and GO helper functions from GOstats to
	Added chrCats() and other functions from iSNetwork
	Removed obsolete data objects and added more interesting
	Updated vignettes to describe new ExpressionSetIllumina objects
	Added method for calculating Illumina differential expression
	Added S4 methods and documentation

	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
	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)
AA_ALPHABET constants and the 'alphabet' method for AAString objects
	Moved GOHyperG back to GOstats
	Renamed slots pvalue.cutoff => pvalueCutoff, test.direction =>
	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
	Added function to perform B score normalization, and for
plotting the spatial effects

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