July Changes in BioC Devel

    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