February Changes in BioC Devel

    February 2007

ABarray
    Modified to use ExpressionSet instead of exprSet

affxparser
   
    Now readCelunits() can handle unit groups for which there are
    no probes, e.g., when stratifying on PM in a unit containing
    only MMs.

    Added writeCdfHeader(), writeCdfQcUnits() and writeCdfUnits(),
    all of which are used by writeCdf(). They make it possible to
    write a CDF in chunks using bounded memory.
   
annaffy
    Updated AmiGO URL
   
beadarray

    Changed structure of class BeadLevelList to handle uneven
    numbers of beads per array, and two-colour data. Updated
    plotting and summarising functions.
   
    Added boxplotBeads(), arrayNames(), numBeads(), getArrayData()
    to work on this class.

    New function readIllumina() to read in raw bead-level data.


Biobase
   
    Added experimental unsaveSetSlot for internal use. This
    functiona llows one to set the slots of an S4 object in place
    without any copying. This should allow for considerable speed
    up when used appropriately.

    Added ExpressionSet introduction vignette. Moved old Biobase
    vignette to new 'legacy' directory.

    Disallowed drop = TRUE for AnnotatedDataFrame.

biomaRt

    Added port attribute to listMarts() and useMart() so users can
    choose which port to connect to when using biomaRt in MySQL
    mode. Changed default Ensembl host to martdb.ensembl.org using
    port 3316.
   
    Added retrieval of more sequence types with the getSequence
    function (such as retrieval of exons and upstream
    sequences). One can now also use filters for the type argument
    of getSequence(). Removed getXref() and getPossibleXrefs() as
    these have been deprecated by getBM() and getLDS(). Removed
    the martTable object as ouput from all functions is now a
    data.frame.

Biostrings

    Added the Boyer-Moore algorithm. The defaults for
    matchPattern() are now fixed = TRUE and the 'auto' feature ow
    picks up the 'boyer-moore' algorithm whenever possible
    (generally faster than the shift-or algorithm.

    Added the 'naive' algorithm for QC and as a benchmark.

    Added the 'gregexpr' algorithm when pattern and subject are
    both standard character strings. The 'gregexpr' algorithm is a
    modified version of the standard R gregexpr(), to be used as a
    'pure R' benchmark.

    Changed modified gregexpr() to gregexpr2() and added
    gregexpr(). Both undocumented.

    Terminology changes. The 'Strong Good Suffix shifts' are now
    called the 'Very Strong Good Suffix shifts' to indicate the
    difference (>=) from the usual Strong Good Suffix shifts. The
    'Good Right Shifts' are now called the 'Matching Window
    shifts'.

   
Category
   
    Added ability to run huperGTest() using chromosome bands as
    categories. This adds the ChrMapHyperGParams and
    ChrMapHyperGResult classes and code.

    Improved handling of MAP annotation ranges. Instead of
    dropping annotations given as a range of chromosome bands, we
    now take the longest common prefix. There are still some
    inconsistencies in the annotation which we don't handle
    perfectly.
   
    Removed unused geneCounts and universeCounts from HyperGResult
    object. Methods with the same names are available for
    accessing these data from the result object. Thanks to N. Le
    Meur for the bug report.

cellHTS

    Added two new summaries that can be used in
    summarizeReplicates(), 'closestToZero' and 'farthestFromZero'.

EBImage
   
    Bug fix: memory of the size of unpacked image was lost on
    every operation using ImageMagick built in filters. Other
    filters were not affected, nor were IO, conversions or object
    detection. Everyone using the package should update to this
    version.

    Added propagate(), a Voronoi-based segmentation on image
    manifolds with modified metric.

exonmap
   
    gene.details(), transcript.details() and exon.details() now
    take a vector as input and return a data.frame (as
    advertised). pc() now uses rowttests(), and does not need
    members to be specified if factor has exactly two levels.

    Added gene.strip() and probesets.in.eset().

    Improved scale on plot.gene().

gcrma

    Changed optical background correction to tolerate no MM
    arrays.
   
graph
   
    Added edgeMatrix method for graphAM.
   
    Fixed graphNEL ==> graphAM by removing rownames from
    adjMat. The optimized version was resulting in a graphAM
    instance with rownames and colnames on the adjMat. The graphAM
    initialize method removes rownames so the node names are
    stored once.

    Fixed bug in ftM2graphNEL() that was due to partial string
    matching in accessing list elements by name.

limma

    normalizeRobustSpline() now works with only one print-tip
    group. New function mergeScahsRG().

    Deprecated getColClasses() and namesInFun() and replaced with
    read.columns(), a more general function that is similar to
    read.delim() but reads specified columns only. Argument '...'
    added to all as.matrix methods for compatibility with R-2.5.0.

    Bugfix: lm.series() and gls.series() were returning errors
    when the design matrix was not of full rank and the columns
    were names.

    Bugfix: write.fit() was using ambiguous column names for the
    coef, t-statistic and p-value when the MArrayLM object had
    only one column and these components were matrices with one
    named column.

    Default for digits changed in write.fit().


lumi

    Updated lumiR() to allow directly adding nuID when reading the
    data, and updated addNuId2lumi to add the tracking history.

    Updated the combine method of LumiBatch class, addNuId2lumi(),
    lumiR() for better adaptiveness.

pcaMethods

    Added support for non-linear PCA and made corresponding
    additions to the documentation. Also added simulated example
    data for use with nlpca(). Changed Q2 cross-validation to
    guarantee that no full column or row is ever deleted. The
    screeplot() function was removed and replaced with plotR2().

    K-estimate now supports NMRMSEP and Q2 as error measure.

    Upgraded plotPcs() so it works with Sweave() and gives
    prettier output by basing it on pairs() instead of slplot().

    Added a new method kEstimateFast(). This also estimates the
    best number of components/similar genes for missing value
    estimation. In contrast to kEstimate() no crossvalidation is
    performed. This is a more rough estimate than provided by
    kEstimate().

    Improved speed of kEstimate(). Now possible to get the
    estimation error for each individual incomplete variable. This
    allows one to easily see for which variables missing value
    imputation makes sense.

    Removed ellipse dependency.

    Added vignette on missing value estimation.

    New method to comvert pcaRes to exprSet. pca() no longer
    returns an exprSet if an exprSet was used as input, use
    asExprSet() instead.


simpleaffy

    Added C. elegans and yeast2 to data for QC stats. Updated to
    work with ExpressionSet class.


vsn

    Improvements on the predict method for vsn(). justvsn() is now
    exported.
   
    Updated lymphoma dataset to ExpressionSet.
   
    Made vsn2() compatible with limma package.

    Updated vignette.