[Bioc-devel] NEWS July 2006

[James MacDonald]

	July 2006

ABarray
	Modified matrixPlot.R to solve problems with fig margin too
large

affxparser
	Improved the speed of updateCel()

affy
	Changes to MAplot for AffyBatch
	Bug fix to the title for image()
	
affycoretools
	New functions
	limma2biomaRt - emulates limma2annaffy, but gets annotation data
using the biomaRt package
	vennSelectBM - emulates vennSelect, but uses biomaRt
	probes2tableBM - emulates probes2table, but uses biomaRt
	foldFiltBM - emulates foldFilt, but uses biomaRt
	linksBM(), annBM() - helper functions used to determine what
data are available at a BioMart

affyio
	Better CEL file corruption testing for binary files

affyPLM
	log-scale mean == geometric mean may be used for determining
scaling amounts for scaling normalizations
	Updates to MAplot function
	Added vignette explaining the MAplot function
	Added hist() for exprSet

annaffy
	Bug fix to remove dependence for automagic download of required
files on reposTools. The dependence has been moved to Biobase

AnnBuilder
	Problem with base file being GIDs fixed
	When baseMapType is "refseq", use gene2refseq instead of
gene2accession to get Entrez Gene ID
	Bugfix when baseType is 'll', AnnBuilder had problems generating
go2probe and go2allprobe mappings

annotate
	Bugfix for getQuery4UG, where UniGene IDs with > 2 letters in
the name (such as for C. elegans) were not being used


AnnotationDbi
	Added a vignette and some utility functions

aroma.light
	New Package:
		Methods for microarray analysis that take basic data
types such as matrices and lists of vectors.  
		These methods can be used standalone, be utilized in
other packages, or be wrapped up in higher-level classes.
	Maintainer:
		Henrik Bengtsson

beadarray
	Added new vignette
	Added more informative error messages to C code
	Made the createBeadSummaryData() code more robust when given
non-existent probe IDs
	Renamed readBeadImages to readBeadlevelData
	Made readBeadLevelData work with the new Illumina BeadScan
output format

Biobase
	More accurately documented the abilities of combine()
	Added featureNames to exprSet
	Fixed typo in warning for combine
	More efficient implementation of the dims methods for eSet
class
	AssayData more careful about sapply/lapply to avoid unnecessary
copying
	Added userQuery() from reposTools. This is a function to query
an end user with a yes/no question
	Added vignette on eSet and Biobase development

biomaRt
	Added a describe() function to retrieve a description of
attributes and filters
	Fixed getSequence()
	Fixed getHomolog() example and output
	Added virtualSchema to BioMart registry query

cellHTS
	Correction in the color code for controls in the scatterplot
between channels
	The ouput of importFun() was changed from a data.frame to a list
to be more versatile
	Added a step to annotate() where the columns 'Plate' and 'Well'
are ordered
	Reduced the size of the color bar when there are less plates on
the screen
	Updated vignette to explain how miu and sigma are calculated in
formula (3)
	Added functions to go from the 384-well format to the 96-well
format
	Added functions to plot a 384-well plate in the 96-well plate
format
	Added an on.exit(killProgress()) to writeReport() for exception
handling when the function exits with an error
	Show the color for empty wells in the HTML quality report
	
CLL
	New Package:
		The CLL package contains the chronic lymphocytic
leukemia (CLL)
 		gene expression data.  The CLL data had 24 samples that
were either classified
		as progressive or stable in regards to disease
progression.  The data came
		from a lab in Italy.
	Maintainer:
		Elizabeth Whalen

geneplotter
	Bugfix in smoothscatter()

makePlatformDesign
	Added 'alleleAB' and 'middle_base' to the PDenv for SNP chips. 
	Both are factors, with alleleAB mapping the actual SNP to 'A' or
'B', consistent with Affy, and middle_base listing the two possible
bases at the middle position
	
oligo
	Added getM() and getA(), to get the M and A values
	Added crlmm()

pcot2
	New Package:
		PCOT2 is a permutation-based method for investigating
changes in the activity of multi-gene networks. 
		It utilizes inter-gene correlation information to detect
significant alterations in gene network activities. 
		Currently it can be applied to two-sample comparisons. 
	Maintainer:	
		Sarah Song

prada
	Fixed documentation to read.fcs(), and extended it to read in a
series of FCS files


Rgraphviz
	Refactored configure script to require graphviz >= 2.2
	The configure script now respects the --with-graphviz option and
searches for pkg-config and then dotneato-config
	Conditional compilation providing compatibility to old graphviz
versions has been removed
	
Redland
	Added headers to prepare for windows support
	getProperties() dropped
	Improved handling of XML-RPC responses

sigPathway
	Flipped the sign of the 2-sample t-statistics, adjusted help
files to reflect that change.

snapCGH
	Removed findBreakPoints
	Added interactive plotting functions zoomChromosome, zoomGenome,
and IDProbes
	Added readPositionalInfo for automated support for extracting
positional information from RGLists
	Updated vignette to reflect new functionality
	Added functions for comparing segmentation schemes
	Added option for running runBioHMM as a homogenous hidden Markov
model
	Added $method to SegList class
	Rewrote processCGH() to return a SegList
	Edited all segmentation functions to accept either an MAlist or
a SegList
	Adjusted zoomChromosome() to indicate selected region for both
segmented and non-segmented data

SNPscan
	Made legend color white if plotting symbol has size zero
	
spikeLI
	New Package:
		Data validation tests based on langmuir adsorption
theory
	Maintainer:
		Enrico Carlon

tilingArray
	New functions:
	qcPlots - create simple diagnostic plots of the raw probe
intensity data
	segChrom - calls 'segment' function for each strand of one or
more chromosomes
	PMindex, MMindex, BGindex - accesses PM, MM, and background
probe indices from the probe Anno environment
	Updates:
	normalizeByReference - new argument probeAnno allowed. When
supplied, the 'pms' and 'background' probe indices are automatically
extracted from the probeanno
	plotSegmentationDots - when SegObj is supplied, a check is made
ot ensure that there is at least one change-point to be plotted in the
region of interest before grid.segments() is called
	Fixed a bug in readCel2eSet()
	
vsn
	More stringent check of 'p' parameter in vsnh


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