December Changes in BioC Devel

    December 2006

affxparser
    Updated writeCdf() to handle the recent name change (block(s)
    to group(s)). Thanks to Ken Simpson
   
affycoretools
    Added 'legend' argument to plotPCA() to allow end users to not
    add a legend
    Added functionality to pass a matrix to plotPCA()

affyPLM
    Many modifications to convert PLMsets from exprSet to
    ExpressionSet

AnnBuilder
    Added Illumina annotation package descriptions

AnnotationDbi
    Added makeDataPackage() method for SQLiteAnnDataPkgSeed
    objects
    Improved makeDataPackage() - added unlink argument, create
    directory if it doesn't exist
    Added sqliteVersion argument to makeDataPackage(). The default
    is the version of the last available RSQLite package from CRAN
    Added AffySNPPDInfo class
    Code for PDInfo moved to oligo package
    Added db() accessor method

Biobase
    Improved handling of unknown arguments in eSet's initialize
    method. We put unknown arguments passed in via '...' into
    elements of assayData. We attempt to assign these elements to
    slots and only if no such slot is found does the argument end
    up in assayData. The reason to do this is to allow subclasses
    to rely on default initialize method behavior where extra
    arguments are treated as slot initializers.
    Added more extensive documentation for combine(), AssayData,
    AssayData-method
    Added methods to annotatedDataFrameFrom(), to initialize from
    'matrix' and NULL
    Allow ExpressionSet to pass '...' through to eSet, where
    arguments are either added as class slots or assigned to
    assayData. Modify eSet handling of '...' so that slot
    arguments are always assigned. Check that assayData members
    are valid as they are assigned to assayData, to avoid cryptic
    error messages.
    Better error message for sampleNames<-, AssayData-method
    Improved error message for createPackage() when destDir
    doesn't exist
   
biomaRt
    Removed cleanBM() function, fixed bug in getGene() when used
    with mmusculus dataset. Updated getHomolog() so it returns
    both the identifiers used in the query and the identifiers of
    their corresponding homologs (this wil only work from Ensembl
    v42).
    Enabled getBM() queries without filters
    Added a verbose argument to getBM() to display the XML or
    MySQL queries that are executed
   
Category
    Fixed formatting of size column in htmlReport output to
    integer
    Added validation method to HyperGParams - we now check that
    geneIds and universeGeneIds have no duplicates, that geneIds
    is a subset of universeGeneIds, and that the pvalue cutoff is
    between 0 and 1.
   
cellHTS
    The progress report window can now be switched off
    More comfortable treatment of plotPlateArgs parameter

cosmo
    Calls to round() in C code were replaced by NINT() to make
    code more portable
    Problems in the computation of the AIC and BIC criteria were
    fixed

EBImage
    New version of EBImage, fully recoded - should now run on
    Windows as well, if the dependencies are satisfied
    The new code is much cleaner and less buggy, using only C
    rather than C++
    Added precompiled windows dll to make compiling on windows
    easier
   
flowCore
    Added a convenience constructor for rectangular gates called
    rectGate().
    Added a %in% method to flowFrame() for rectangular gating
    Changes to filter() to make it a single function that
    dispatches the appropriate %in%
    New vignette that outlines the use of filters
    Added a summary() method primarily for filterResult objects
    Added a print() method for summaryResult objects
   
globaltest
    Enabled vector of Entrez Gene mappings as annotation in
    makeGOstructure()

GOstats
    Deprecated getGoGraph - it was meant for internal use only
    Added extensive details to GOstats vignette. Added description
    of input arguments. Showed details of input
    arguments. Explained why parameter object design is
    useful. More details about output and available accessor
    functions.
   
limma
    Bug fix to arrayWeights() to correctly ahndle design matrices
    that do not have full column rank
    Updated arrayWeights() man page
    Added new function printtipWeights() that returns sub-array
    quality weights
    New function as.matrix.ExpressionSet()
    Section on array quality weights added to User's guide
   
oligo
    Added PDInfo classes. These represent platform design
    information (chip description with some
    annotation). Subclasses support PDInfo objects backed by
    SQLite DBs, but allow for transitional compatibility with
    environment based PDInfo subclasses.
    Added capablities to use BufferedMatrix objects in assayData
    of *FeatureSet objects (only for Affymetrix now).
    Added read.celfiles2() and rma2() to use BufferedMatrix objects.
    Modified pm() to return a BufferedMatrix.
    Many modifications to get CRLMM working on SQLite-based PDInfo
    objects

pcaMethods
    Major update. Added llsImpute() to allow better rating and
    comparison of the obtained results, based on Kim et al.,
    Bioinformatics 2005 (for details, see documentation)
    Added nniRes(), a nearest neighbor imputation.
    The threshold in ppca() was changed to 1e-5
    Replaced maxPcs with evalPcs in kEstimate() - user can now
    enter a vector of arbitrary integers
    The pca() function now includes the nni method

Rgraphviz
    Updated to work with Graphviz 2.10 and 2.12