May changes in BioC Devel

    May 2006

affyPLM
    ReadRMAExpress() now handles gzipped input
   
affxparser
    Updated to use Affy's new SDK
    Adding ability to read BPMAPS
   
AnnotationDbi
    Added a slightly different version of dbGetQuery(), which doesn't do data type conversion for the result

Biobase
    Added compatibility layer for old version of cache(), so foo <- cache("foo", someExpr) still works with a deprecation warning
    Added Versions, VersionsNull, Versioned, and VersionedBiobase classes
    Renamed AllClasses to DataClasses to accomodate need to first load Version-related classes and methods
    Modified updateObject methods to first check isVersioned before isCurrent
    Added dependency on utils so winMenuAddItem() can be found if Biobase is loaded
    Modified updateObjectFromSlots() to use lapply() rather than sapply() to avoid oversimplification
   
beadarray
    Updated class definitions
    Rewrote functions readBeadImages() and createBeadSummaryData() in C to increase speed by a factor of 10 and remove need to convert tiff images to pgm
   
BufferedMatrix
    Added is.BufferedMatrix() and as.BufferedMatrix()
   
cellHTS
    Updated writeReport() to return full path and name of report index file
    The column 'Position' is no longer mandatory in the plate configuration file; readPlateData() automatically detects the plate format from the raw intensity files
    New function normalizePlates() to correct for plate effects
    writeReport() now prints some status indication while creating the per-plate and experiment HTML reports
    Added the root mean square as an option to summarize across replicates
    writeReport() allows one to specify the name of the controls, because there may be distinct controls for different reporters
    The positive and/or negative controls can also be specified when calling normalizePlates() with 'POC' and 'NPI'
    Added importFun argument to readPlatedata() so other functions can be defined to import the raw data files
    Fixed a bug in writeReport() (missig posControls, negControls when x was not configured)
    Added method writeTab()
    Added a progress bar when calling writeReport()
    Deprecated the argument plateType in readPlateData()
   
CoCiteStats
    Fixed bug in twowayTable() - when Entrez Gene IDs have no papers citing them, we now return appropriate zero counts instead of a subscript error
    Speed improvement for gene.geneslist.sig()
   
copa
    Bugfix in copaFilter() to guard against genes where all genes have the same value

EBImage
    Added plot() as alternative to display() for MacOS
    Added drawables
   
edd
    Fixed edd() so that user specified distList will get used
   
gaggle
    New Package:
        R Goose functions
    Maintainer:
        Paul Shannon

gcrma
    Bug fix in justGCRMA() - one of the .Call() functions was pointing to the affy package instead of affyio
   
genefilter
    Added half_range_mode, a new function from Richard Bourgon
   
geneplotter
    Fixed bug in Makesense so it respects subsetted exprSets
    Default color for plotChr() changed from blue to black
   
graph
    Fixed bug in eWV() by updating to the edgeData system
    More consistent graphAM <-> matrix; graphNEL <-> matrix
    Simplified graphNEL to matrix
    If a 'weight' edge attribute is present, graphAM to matrix coercion puts the edge weights into the non-zero matrix elements
    Fixed bug in inEdges() for graphAM; for undirected graphAM objects we were returning a matrix instead of a list
    Fixed bug in edgeData() when only 'to' is specified
    edgeData() no longer returns a warning when asked about nodes that have no edges when only 'from' or 'to' is specified
    Fixed edge weight handling bug in graph2SparseM() and sparseM2Graph()
    Added 'edgemode' argument to sparseM2Graph(). The default is now a directed graphNEL instance
    Fixed bug in edgeWeights() for graphs with no edges
    Improved documentation for edgeWeights() and added checking for non-vector weight edge attribute
    Removed myCheckException(). The new version of RUnit probides a silent = TRUE arg to checkException that we use instead
    Added optional arguments and type checking to edgeWeights.

hexbin
    Bug fix in hexVP.abline() with col argument, thanks to Scott Chaslow
   
limma
    Bug fix (reported by Al Ivens); when B635 SD or B532 SD = 0 for a spot, division by zero occurs in .expectedBayesianFG - when this occurs, no background correction is now done for that spot
    New function plotFG() for foreground-background plots
    Bug fix in kooperberg()
    Bug fix in read.maimages(); using readGenericHeader() to get column names was not working when sep or quote were different from defaults - now using scan() to read column names
    Bug fix to plotAM3by2() which was not passing on the setting of the zero.weight arguments to plotMA()
    Bug fix to read.imagene(), which was trying to read too many data rows when there were multiple ImaGene fields
   
MVCClass
    Added some new classes and changed some existing classes, includes doc changes
   
rflowcyt
    Added function to convert cytoFrame(prada) to FCS
    Updated read.FCS() functions and added coerce methods
   
sigPathway
    New Package:
        Pathway Analysis
    Maintainer:
        Weil Lai
SNPscan
    Major changes to make package compatible with SNP annotation packages and latest BioC release

xcms
    Fixed bug where NetCDF files wouold hav etheir scans incorrectly reversed
    Merged recent changes to RAMP mzXML/mzData parser to support TimeInMinutes