[Bioc-devel] NEWS August 2006

[James MacDonald]

	August 2006

affxparser
	Added trial version of updateDelUnits()
	
affycoretools
	Fixed buglet in annBM() that didn't list 'Symbol' as something
that could be annotated if passed with a mart argument
	Added vignette for new biomaRt based functions
	Removed celfiles from /examples directory, replaced with .Rdata
files, to make package download quicker
	Bugfix in getStat() where the 'tstat' argument wasn't working
correctly
	Fixed bugs in affycoretools vignette
	Modified plotDeg() to put the legend on the right instead of on
top of the plotted lines

affyPLM
	Small fix to boxplot() when applied to a PLMset containing a
non-default model
	Fixed a problem with a model of the style PM ~ -1 + samples +
treatment:probes being misidentified as the default model
	
AnnBuilder
	Included Gallus gallus (chicken)
	Updates to athPkgBuilder:
		Changed data source for probe-to-gene mapping, PubMed
annotation
		Added annotation from KEGG - now environment 'PATH' is
annotation from KEGG
		Annotation from AraCyc is stored in environment
'ARACYC'
		Added function getFileExt() to auto-generate the value
for parameter fileExt in athPkgBuilder()
		baseName can be missing - uses default mapping from
ftp://ftp.arabidopsis.org/home/tair/Microarrays/Affymetrix/ 
		Added a parameter 'indexby', value is either 'PROBE'
(default) or 'ACCNUM' - if it is PROBE, all annotations are indexed by
probe ID, if ACCNUM, they are indexed by AGI locus ID
	
annotate
	Updates to work with eSet/ExpressionSet class
	Bugfix in htmlpage() that wasn't handling list length checking
correctly. Thanks to Laurant Buffat for pointing this out
	
arrayQCplot
	New Package:
		Explore microarray data and check quality and
reproducibility.
	Maintainer:
		Eun-kyung Lee

beadarray
	Changed readBeadLevelData() to read single and two channel data
in the new BeadScan format
	Made $G the name for single channel data (rather than $R)
	Added BLImagePlot which produces a bead level image plot
	Improved BLImagePlot with arguments for the color of high and
low intensity areas.
	
beadarraySNP
	New Package:
		Importing data from Illumina SNP experiments and
performing copy number calculations and reports.
	Maintainer:
		Jan Oosting

Biobase
	Changes to vignette on eSet and Biobase development
	Exported selectSome for use in GGtools
	Fixed bug in cache() preventing use from inside a function
	
biomaRt
	Changed the output of listAttributes() and listFilters() to a
data.frame where the first column is the attribute/filter name, and the
second column contains the description
	Updated vignette
	Changed the default output of listMarts to a data.frame only
containing the name and version of available BioMart databases
	Fixed bug in getSequence() when used in MySQL mode

Biostrings
	Fixed vignettes and examples to use the new 'Biostrings-based
genome data packages'

BSgenome
	Renamed the GenomeBase package to BSgenome to match resulting
data packages
	Replaced BStringGenome class by more general BSgenome class
	Added 'prefix' and 'suffix' arguments to buildDataFiles()
function

Category
	Removed default value for 'lib' argument in GOHyperG. The
default was 'hgu95av2' and if people didn't change it, they would get
unexpected results
	Added pvalue.cufoff slot to GeneCategoryHyperGeoTestResult
class
	Refactored hypergeometric testing code
		Added base class for test result
		Added accessor methods for result classes
		Rationalized return result
		We now keep the category to gene ID mapping and compute
the counts on it
	
cellHTS
	Modifications to allow one to have a single plate in the cellHTS
object
	Small correction in vignette; summarize replicates using mean
instead of RMS
	Added a basic function to get a matrix with replicate values for
a given channel in columns, given an array of raw or normalized
intensities
	
clusterStab
	Added methods for ExpressionSets
	
	
copa
	Added S4 methods for input objects

geneplotter
	smoothScatter() and densCols can now also work with NA values
	
GEOquery
	Fixed getGEOfile() to reflect new URL for GDS raw data
	Changes to GDS2MA() and GDS2eSet() to deal with NULL in GDS
datatable
	
GGtools
	New Package:
		Software and data for genetical genomics, dealing with
hapmap SNP reports, GWAS, etc.
	Maintainer:
		VJ Carey

GOstats
	Added conditional GO hypergeometric algorithm
(goHyperGeoTest())

lapmix
	New Package:
		Laplace mixture modelling of microarray experiments. 
		A hierarchical Bayesian approach is used, and the
hyperparameters 
		are estimated using empirical Bayes. The main purpose is
to
		identify differentially expressed genes.
	Maintainer:
		Yann Ruffieux

limma
	CARMAweb reference added to User's guide
	In read.maimages(), flush = TRUE added to all instances of
read.table(), making read.maimages() tolerant to spurious columns at the
end of data lines
	Added 'cutoff' argument to wtflags(), argument 'w' renamed
'weight'
	Added Fitted Model Objects to User's guide
	read.imagene() uses mean background instead of median if the
auto segmentation method has been set
	readImaGeneHeader() updated to allow for extraneous trailing
white space in the lines of data files
	In geneSetTest(), values "two.sided", "less" or "greater" are
now permitted as synonyms for "either", "down" or "up"
	geneSetTest() no longer issues warning with type = "t", and all
positive values for statistic
	New function as.matrix.PLMset(), allowing lmFit() to work
correctly on PLMset objects
	Bob case study updated in User's guide
	New argument 'coefficients' for contrasts.fit(). This provides a
simple way to specify the contrast matrix when the contrasts are just a
subset of the original coefficients.
	New function topTableF() to rank genes on the basis of
F-statistics
	normalizeWithinArrays() was incorrect with method="composite"
and weights=NULL, now fixed.
	makeContrasts() now gives informative error message if parameter
names are not syntactically valid.
	New argument 'contrasts' for makeContrasts() which will accept a
character vector of contrasts. 
	The matrix produced by makeContrasts() now has named dimensions
	New function exprs.MA() to extract log-expression matrix from
MAList
	
maDB
	Changes in writeTable(), fixing problems with annotation
packages that don't provide all annotation sources

made4
	Bug fix in bga(), so one can now plot results bga.suppl so that
the coordinates of the new test projection are plotted onto the results
of bga (as in Fig 3 of Culhane et al., 2002)

pkgDepTools
	New Package:
		Tools for examining package dependencies
	Maintainer:
		Seth Falcon

ppiStats
	New Package:
		Protein-Protein Interaction Statistical Package -
Package to analyze Bait to Prey Data Sets
	Maintainer:
		Tony Chiang
quantsmooth
	Improved handling of sex chromosomes in
prepareGenomePlot.html()
	
SAGx
	New Package:
		A package for retrieval, preparation and analysis of
data from the Affymetrix GeneChip. In particular the issue of
identifying  differentially expressed genes is addressed.
	Maintainer:
		Per Broberg

snapCGH
	Added function nudSegmentation() for highlighting regions of
gain, loss, amplification and deletion.	
	Fixed functionality of readPositionalInfo() when using Nimblegen
data

splots
	New Package:
		New small utility package with the emphasis on minimal
dependencies for visualizations for high throughput screens
	Maintainer:
		Oleg Sklyar

tilingArray
	Added ability to plot segment boundaries on heatmap plot when
seqObj specified
	Fixed background index bug in normalizeByReference()
	
weaver
	New Package:
		This package provides enhancements on the Sweave()
function
 		in the base package.  In particular a facility for
caching code chunk
		results is included.
	Maintainer:
		Seth Falcon

xcms
	Fixed bug where xcmsSet() failed if less than two peaks were
detected in a file
	Added warning to scmsSet() if less than ten peaks were detedted
in a file

	




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