August Changes in BioC Devel

    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