[Bioc-devel] NEWS - September 2006 (Redux)

[James MacDonald]

The first time was a bad cut&paste job, and the line breaks were
unfortunately off...

	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
	Changed how Bscore function is called; it can now be called
directly or using normalizePlates() 
	 or normalizeChannels()
	Added an example for a two-way assay and the respective
vignette
	Added a plate normalization that consists of scaling by the
median intensity of the negative 
	 controls
	Added a function to determine the overlap between the gene
annotation of two screens
	
EBImage
	Bugfix to allow display() to work via SSH and probably on MacOS
(latter untested)
	Added mehtod tile(Image, width, ...) to arrange images in a
stack tiled on a single 2D image
	
gaggle
	Added a convenience function test.map1() for testing hashmap
broadcasts

genefilter
	Added genefinder methods for ExpressionSet objects

GeneMeta
	Added ExpressionSet method for getdF()
	
geneplotter
	Added example how to use smoothScatter with 'pairs'
	
GOstats
	Added odds ratio calculation for hypergeometric test
	Added a summary method for HyperGeoTest objects that returns
result in a data.frame
	Added htmlReport method for HyperGeoTest objects to return
result as an HTML table
	Moved isConditional generic to Category
	Moved GOusage vignette and GO helper functions to annotate
	Moved hasGOannotate to annotate
	Added function probeSetSummary() to list probesets responsible
for significance of GO terms
	Deprecated hyperGTable() (replaced by summary method for
HyperGeoTest objects)
	Deprecated hyperG2Affy() (replaced by probeSetSummary())

graph
	Removed dependency on Ruuid (removes graphH, gNode, gEdge
classes, which appear to be unused by 
	 client code)
	Only load Biobase on Windows
	Bugfix to vectorization bug in graphNEL removeEdge method.
Thanks to Dan Bebber for reporting 
	 and providing an easy to reproduce test case
	Simplified removeEdge
	Added reverseEdgeDirections
	
limma
	New argument 'lfc' for decideTests() to require a minimum
fold-change
	normalizeWithinArrays() now uses asMatrixWeights() to process
weights arguments. This allows the 
	 weights to be a vector of probe weights, a vector of array
weights, or a matrix of spot weights
	Weights argument of modifyWeights() now has a default value
	topTable() now accepts vector argument coef. If length(coef)>1,
topTableF() is called to produce 
	 a ranking by F-statistic
	New arguments col and lwd for plotlines()
	Improvements to lm.series(), glm.series() and rlm.series() to
better preserve column names.
	topTable() with coef=NULL now ranks genes by F-statistic for all
contrasts
	Warning about 'experimental' now removed from lmscFit man page
	New arguments for vennDiagram() to allow colors and printing of
multiple tests of counts on the 
	 same diagram
	
matchprobes
	Bugfix in matchprobes() 'toupper' was unnecessarily and
undocumentedly called on the argument 
	 'query' (see the posting to BioC mailing list 14 Sep 2006)
	
nem
	New Package:
		The package 'nem' allows to reconstruct features of
pathways from the nested structure of 
		perturbation effects. It takes as input (1.) a set of
pathway components, which were perturbed, 
 		and (2.) high-dimensional phenotypic readout of these
perturbations (e.g. gene expression 
		or morphological profiles). 
		The output is a directed graph representing the
phenotypic hierarchy. 
	Maintainer:
		Florian Markowetz

pcaMethods
	New Package:
		Provides Bayesian PCA, Probabilistic PCA, Nipals PCA and
the conventional SVD PCA.
  		BPCA, PPCA and NipalsPCA may be used to perform PCA on
incomplete data 
  		as well as for accurate missing value estimation.
  		A set of methods for printing and plotting the results
is also provided.
 		All methods make use of the same data structure (pcaRes)
to provide
 		 a unique interface to the PCA results. Developed at the
Max-Planck
  		Institute for Molecular Plant Physiology, Golm,
Germany.
	Maintainer:
		Wolfram Stacklies


	



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