[Bioc-devel] NEWS October 2006

[James MacDonald]

	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



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