CHANGES FOR BioC 2.14 - April 2014

MAJOR CHANGES

    o   An ExpressionSet object can be converted into an ExpressionSetIllumina

    o   An ExpressionSetIllumina object can be converted into a GRanges object, with the ranges derived 
        from the probe positions

    o   The plotMAXY function has been deprecated and replaced by defining the an instance of the generic plotMA for ExpressionSetIllumina

    o   Files suitable for submission to GEO can be created using makeGEOSubmission

    o   A new class for storing limma results; limmaResults

    o   limmaDE: Differential expression analysis can be performed by supplying a SampleGroup vector. All              
        pairwise comparisons are done.

    o   A limmaResults object can be converted into a GRanges


CHANGES IN VERSION 2.4

MAJOR CHANGES

    o   The example data required to run examples and the vignette has been
    removed from the package. The experimental data package beadarrayExampleData
    has been created for this purpose

    o   Mapping of bead-level ArrayAddress IDs to Illumina IDs is now performed by
    loading a companion annotation package. e.g. illuminaHumanv3.db

    o   The addFeatureData function has been added to simplify the annotation of
    summary data objects

    o   The ggplot2 library is now used to produce boxplots of summary data with
    the option of including columns of featureData or phenoData as factors in the plot

    o   The combinedControlPlot has been added, which uses ggplot2 to consolidate
    the bead-level control plots into a single graphic

    o   BASH and HULK can now only operate on a single array at a time and accept
    an outlier-calling method as a parameter


OTHER CHANGES

    o   The imageplot function now uses ggplot2
	
    o   Accessor functions added for metrics, P95 value and signal-to-noise ratio

    o   The default background correction when running readIllumina with 
    useImages = TRUE is now the medianBackground method

    o   getAnnotation replaced with annotation accessor function 

    o   setAnnotation replaced with annotation <- replacement method

    o   checkPlatform replaced with suggestAnnotation function 

    o   The platformSigs object was added and contains lists of ArrayAddressIDs
    for all know expression platforms

    o   The outlier calling method, squeezedVarOutlierMethod has been added, which
    shrinks the observed variance for a bead-type towards the predicted variance
    based on all bead-types on the array-section

    o   Errors in BASH that led to the einvasions and dinvasions arguments not being 
    respected have been corrected

    o   lower-level BASH functions (e.g. BASHDiffuse) will no longer calculate a 
    Neighbours matrix if one is not supplied (ergo one must be supplied)

    o   beadarray used to have problems if no outlier removal method were set in 
    summarization (important if the outliers have already been removed by Illumina's 
    scanner software). The function noOutlierMethod is provided to address this 

    o  findAllOutliersE and findAllOutliersIgnore are to be deprecated, used 
    internally by BASH have been removed

CHANGES IN VERSION 2.3

NEW FEATURES
	
	o	checkRegistration() has been completely re-written to provide a far more
	meaningful result in a new class, beadRegistrationData

	o	beadRegistrationData objects can be passed to boxplot.

	o	The summarize function now has a default channel parameter and useSampleFac = FALSE


BUG FIXES in 2.3.6

	o	Fixed problem when providing arrays argument to checkRegistration()

	o	Fixed problem in readIllumina when useImages = TRUE

	o	Patched error with analyseDirectory() (thanks to Juerg Straubhaar for this)

BUG FIXES in 2.3.6

	o	Fixed problem when providing arrays argument to checkRegistration()

	o	Fixed problem in readIllumina when useImages = TRUE

	o	Patched error with analyseDirectory() (thanks to Juerg Straubhaar for this)

BUG FIXES in 2.3.5

	o	Added support to readIllumina() for files that use something other than
	a period as the decimal point character.

BUG FIXES in 2.3.4

	o	Fixed issues when using a combination of iScan data and a locs file 
	to generate neighbours, manifesting as problems with imageplot and BASH.

BUG FIXES in 2.3.3

	o	Stopped the presence of any other .txt files in a directory resulting 
	in undesirable behaviour of readIllumina()

BUG FIXES in 2.3.2

	o	readBeadLevelTextFile will now take (and use) a seperator argument.

	o	locs information correctly taken from a bab file if required.  This effects
	functions such as generateNeighbours(), BASH(), HULK(), imageplot()

BUG FIXES in 2.3.1

    o   Image processing functions can now be passed matrices containing either
    integer or numeric values.

    o   Passed forceIScan argument to functions called by readIllumina()


CHANGES IN VERSION 2.1

NEW FEATURES

    o   combine methods added for beadLevelData and ExpressionSetIllumina

BUG FIXES in 2.1.16

	o	Fixed problem in BASH that could cause a segfault.

BUG FIXES in 2.1.12

    o   Modified show method for beadLevelData class, so it doesn't fail when 
    the user has added their own section data.

BUG FIXES in 2.1.5

	o	Metrics read automatically when section names are specified in readIllumina()

	o	Correct section names are retained when summarizing multiple chips.

BUG FIXES in 2.1.4

    o   Fixed problem with imageplot when a small value for the squareSize argument 
    resulted in a crash (thanks to Ying Wu for supply the patch) 

BUG FIXES in 2.1.3

    o   Corrected method names in .Call access to image processing functions

	o   HULK() returns values on the scale specified by the user

	o   HULK() accepts transformation argument

BUG FIXES in 2.1.2

    o   BSData now displays correctly when created from BeadStudio output

    o   setWeights behaves properly when given single array argument

    o   showArrayMask re-instated in package

    o   HULK manual page gives correct definition of funtion output

BUG FIXES in 2.1.1

    o   readBeadSummaryData error when qcFile is missing (FIXED)

    o   readIllumina, imageplot, boxplot accept '...' arguments


CHANGES IN VERSION 2.0

NEW FEATURES

    o   new beadLevelData class to represent bead-level data (replaces beadLevelList class)

    o   beadLevelData includes a sectionData slot for managing per-section data

    o 	readIllumina will store file paths of sdf and locs files

    o 	arrayNames is replaced by sectionNames

    o 	getBeadData replaces the functionality of getArrayData

    o 	insertBeadData may be used to modify the per-bead data in the beadLevelData object

    o 	insertSectionData may be used to modify the per-section data in the
    beadLevelData object

    o 	functions such as logGreenChannelTransform are used to transform the 
    data in the bead-level object, rather than using the what argument

    o 	the 'what' argument in various plotting functions is replaced by a 
    transformation function (e.g. logGreenChannelTransform)

    o 	the backgroundCorrectSingleSection is used instead of backgroundCorrect

    o 	the boxplotBeads function is removed and the generic boxplot is used for beadLevelData

    o 	imageplot and outlier plot functions include a horizontal to change
    orientation of the plot to match the orientation of the original TIFF image

    o 	the squareSize parameter is now used to control the resolution of imageplots

    o 	the imageplot function will attempt to read sdf information to determine
    the optimal values of squareSize

    o 	the checkRegistration function checks for possible errors in the 
    registration of the original image. NB requires locs information to be available.

    o 	the BASH function now returns a QC list item containing the number of masked
    beads and extended score for each array

    o 	BASH function will accept a transformation function argument instead of 'what'

    o 	control probe annotation for Humanv4 arrays is added to ExpressionControlData

    o 	a 'controlProfile' data frame can be used to make control plots of data
    which are not defined in ExpressionControlData

    o 	the quickSummary and makeQCTable functions are added to summarize various
    control types on specified arrays

    o 	the controlProbeDetection function returns the percentage of beads belong
    to defined set of control types that are expressed above background

    o 	the calculateOutlierStats function returns the percentage of outliers
    that occur in each segment of a particular array 

    o 	the expressionQCPipeline function replaces calculateBeadLevelScores

    o 	the summarize function is used instead of createBeadSummaryData. It 
    requires the specification of an illuminaChannel object which defines the 
    transformation to be applied, outlier function, functions for averaging and a name

    o   the numeric ArrayAddressIDs used in the bead-level data may be re-mapped
    to Illumina IDs (ILMN_...) if the annotation slot of the beadLevelData is 
    present. Probes that cannot be mapped may be removed.

    o 	the sampleFac and useSampleFac arguments to summarize are to be used in 
    circumstances when we wish to combine data from multiple sections. i.e. for 
    infinium data when the SNPs interrogated are spread over multiple sections. 
    The sampleFac argument may be left blank when the sdf file is available.

    o 	different summarization schemes are supported in the summarize function, 
    in which case an ExpressionSetIllumina that incorporates the concept of 
    channels will be created. 

    o 	the readBeadSummaryData functions will read extra annotation columns from
    BeadStudio output

    o 	the NoBeads slot in ExpressionSetIllumina has been re-named to nObservations

    o 	control probes are no longer stored in the QC slot of the ExpressionSetIllumina 
    object, but are in the main exprs matrix along with the gene probes

    o 	support for neqc (limma) and rsn (lumi) in normaliseIllumina


