March changes in BioC Devel

    March 2006

affxparser
    Added findCdf() to search for CDF file of a given chip type
    Added argument 'readCells'to readCdfUnits() to return zero-based cell indices calculated from the (x, y) coordinates
    Added applyCdfGroups(); this function can be used to rearrange the unit groups and their contents of a CDF structure
    Added readCdfUnitsMap() to create an optimized order to read/store cell elements
    Added readCelUnits() to read CEL data by units
    Updated examples in man pages to read data if necessary files are found, to allow users to test examples on their own CDF and CEL files
    Added inst/HISTORY to show users what the changes are
    Added readCelRectangle() to read probe signals from a specific area of the chip
    Known bug: at least on WinXP, heavy use of readCelUnits() will sooner or later core dump R
    
affy
    Removed all parsing C code to affyio
    Fixed bug in just.rma() due to change in parsing code
    
affycoretools
    Added a foldFilt argument to both vennCounts2() and vennSelect() to allow for additional filtering based on fold change
    Bugfix in limma2annaffy() that arose because topTable() in limma now outputs a p-value as well as an adjusted p-value column
        
annaffy
    Added all, all.x and all.y options to merge.aafTable()
    Added custom getHTML method to aafUniGene to fix small bug
    Added is.annpkg() to check to see if a package contains annotation

apComplex
    Added wsVal argument to mergeComplexes() and findComplexes() to allow manual setting of the work space value in Fisher's exact test

biomaRt
    Changed host from www.ebi.ac.uk to www.biomart.org
    Fixed bug in getXref()
    Added a useful error message when getBM() returns NULL due to downtime of webserver
    Enabled list as output for getBM()
    getGene()getGO)getOMIM()nd getINTERPRO()ow also return teh query id when used in HTTP mode
    
Biostrings
    Complete refactoring of this package. Please see NEWS and CHANGES file in package for more information

Category
    Modified findAMstats() so it will keep the rowname of Amat in the result
    Moved GOHyperG from GOstats package
    
cellHTS
    Correction in format() function for adding Biomart results to x$geneAnno
    Correction in the subGraph call
    Removed dependence on biomaRt
    The type of assay is now taken into account when summarizing between replicates, so taking 'minimum' as a summary is always conservative
    readPlateData() is no longer case sensitive to the extension of readout files
    Added plate median scaling for 2-color data
    Added summarizeReplicates(), a function to obtain a single score per probe using the normalized replicates
    
cghMCR
    New Package:
        Based on the algothrim proposed by Dr. Linda Chin's lab, this
          package provides functions that identify chromosome regions that show
        gains/losses commonly observed across different samples profiled using
        arrayCGH platform.
    Maintainer:
        Jianhua Zhang

copa
    Added copaTable() to make a table summary of outlier pairs
    Added scatterPlotCopa() to make a scatterplot
    Fixed bugs in copaPerm() and added a permutation counter

genefilter
    Moved findLargest() from Category package to genefilter
    
geneplotter
    Fixed imageMap signature bug
    
GeneR
    Fixed bug in revComp(force = TRUE)
    
GOstats
    Fixed bug in GOHyperG that gave wrong p-values when universe argument was specified
    Added a universe argument to hyperGtable() and hyperG2Affy()
    Moved GOHyperG to Category package
    
graph
    Added C code for setting attrDataItems to speed up creation of graphs with many node or edge attributes
    Disallowed duplicates when using addEdge() on a graphNEL
    Vectorized removeEdge() for graphNEL
    Refactored subGraph() and initialize for graph with no edges in graphNEL
    Added C code to speed up isAdjacent method
    Fixed order of return value bug in edgeWeights
        
Heatplus
    New Package:
        Add an extra graphical display at the bottom of a heat map,
         indicating for each column a) whether it has one of several binary properties
         or not, and b) the value of a quantitative variable. A cutting threshold for
         the sample dendrogram can also be specified, and the resulting clustering of
         the columns is indicated by coloring both the dendrogram and the extra variable
         display.
    Maintainer:
        Alexander Ploner

idiogram
    Name change from ideogram
    
iSNetwork
    Added to the vignette
    Made chages to the code so multiple graph plots are linked

limma
    Replaced use of La.chol() with chol()
    Bugfix to topTable; separate raw and adjusted p-values were failing when some p-values were missing
    Bugfix: read.maimages(source = "imagene") was confusing a data.frame of file names with a targets file
    Edited and expanded man page for normalizeWithinArrays
    Support for ScanArray Express was added to read.maimages()
    Now reads BlueFuse 3.2 correctly
    
macat
    Modfied preprocessedLoader() to create a valid exprSet before calling annotate package
    
maCorrPlot
    New Package:
        Graphically displays correlation in microarray data that is due to
         insufficient normalization
    Maintainer:
        Alexander Ploner

made4
    Bug fix in bet.coinertia()
    
makecdfenv
    Removed all parsing C code to affyio

makePlatformDesign
    Fixed reading of multiple well arrays NGS
    Added BPMAP capabilities
    Bugfix in how probes are called PM or MM
    Started adding documentation
    
metaArray
    Vignette revised
    
nudge
    New Package:
        Package for normalizing microarray data in single and multiple replicate experiments and fitting a normal-uniform mixture to detect differentially
         expressed genes in the cases where the two samples are being compared directly or indirectly (via a common reference sample)
    Maintainer:
        N. Dean

OCplus
    New Package:
        This package allows to characterize the operating characeristics of
        a microarray experiment, i.e. the trade-off between false discovery rate and
        the power to detect truly regulated genes. The package includes tools both
        for planned experiments (for sample size assessment) and for already
        collected data (identification of differentially expressed genes).
    Maintainer:
        Alexander Ploner

RBGL
    Updated vignette

RMAGEML
    Added a warning when directory is not the full path (RMAGEML used to crash on this)
    
ScISI
    Updated vignette
    Added getLocOrfs() to return ORFS based on gene annotation of user specified GO nodes and will then restrict to the interactome
    Added numerous scripts and man pages

SNPscan
    Fixed bug in summary() function    
    The assayData slot no longer requires copy number of p-values
    
tilingArray
    Added vignette on assessment of the normalization
    Fixed bugs in normalizeByReference()
    Added 'verbose' argument to normalizeByReference()
    Changed normalizeByReference() so it only uses PM probes
    New function comparisonPlot()
    Added segmentation vignette
    plotAlongChrom() now works properly with S4 segmentation objects and displays confidence intervals
    Moved scoreSegments() and yeastFeatures() to davidTiling
    Added readCel2eSet() and plotPenLL()
    Many vignette updates
    
webbioc
    Added information about porting to Windows