NEWS

---

beadarray 2.4

MAJOR CHANGES

• 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
• Mapping of bead-level ArrayAddress IDs to Illumina IDs is now performed by loading a companion annotation package. e.g. illuminaHumanv3.db
• The addFeatureData function has been added to simplify the annotation of summary data objects
• 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
• The combinedControlPlot has been added, which uses ggplot2 to consolidate the bead-level control plots into a single graphic
• 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

• The imageplot function now uses ggplot2
• Accessor functions added for metrics, P95 value and signal-to-noise ratio
• The default background correction when running readIllumina with useImages = TRUE is now the medianBackground method
• getAnnotation replaced with annotation accessor function
• setAnnotation replaced with annotation <- replacement method
• checkPlatform replaced with suggestAnnotation function
• The platformSigs object was added and contains lists of ArrayAddressIDs for all know expression platforms
• 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
• Errors in BASH that led to the einvasions and dinvasions arguments not being respected have been corrected
• lower-level BASH functions (e.g. BASHDiffuse) will no longer calculate a Neighbours matrix if one is not supplied (ergo one must be supplied)
• 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
• findAllOutliersE and findAllOutliersIgnore are to be deprecated, used internally by BASH have been removed

beadarray 2.3

NEW FEATURES

• checkRegistration() has been completely re-written to provide a far more meaningful result in a new class, beadRegistrationData
• beadRegistrationData objects can be passed to boxplot.
• The summarize function now has a default channel parameter and useSampleFac = FALSE

BUG FIXES in 2.3.6

• Fixed problem when providing arrays argument to checkRegistration()
• Fixed problem in readIllumina when useImages = TRUE
• Patched error with analyseDirectory() (thanks to Juerg Straubhaar for this)
• Fixed problem when providing arrays argument to checkRegistration()
• Fixed problem in readIllumina when useImages = TRUE
• Patched error with analyseDirectory() (thanks to Juerg Straubhaar for this)

BUG FIXES in 2.3.5

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

BUG FIXES in 2.3.4

• 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

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

BUG FIXES in 2.3.2

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

• Image processing functions can now be passed matrices containing either integer or numeric values.
• Passed forceIScan argument to functions called by readIllumina()

beadarray 2.1

NEW FEATURES

• combine methods added for beadLevelData and ExpressionSetIllumina

BUG FIXES in 2.1.16

• Fixed problem in BASH that could cause a segfault.

BUG FIXES in 2.1.12

• 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

• Metrics read automatically when section names are specified in readIllumina()
• Correct section names are retained when summarizing multiple chips.

BUG FIXES in 2.1.4

• 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

• Corrected method names in .Call access to image processing functions
• HULK() returns values on the scale specified by the user
• HULK() accepts transformation argument

BUG FIXES in 2.1.2

• BSData now displays correctly when created from BeadStudio output
• setWeights behaves properly when given single array argument
• showArrayMask re-instated in package
• HULK manual page gives correct definition of funtion output

BUG FIXES in 2.1.1

• readBeadSummaryData error when qcFile is missing (FIXED)
• readIllumina, imageplot, boxplot accept '...' arguments

beadarray 2.0

NEW FEATURES

• new beadLevelData class to represent bead-level data (replaces beadLevelList class)
• beadLevelData includes a sectionData slot for managing per-section data
• readIllumina will store file paths of sdf and locs files
• arrayNames is replaced by sectionNames
• getBeadData replaces the functionality of getArrayData
• insertBeadData may be used to modify the per-bead data in the beadLevelData object
• insertSectionData may be used to modify the per-section data in the beadLevelData object
• functions such as logGreenChannelTransform are used to transform the data in the bead-level object, rather than using the what argument
• the 'what' argument in various plotting functions is replaced by a transformation function (e.g. logGreenChannelTransform)
• the backgroundCorrectSingleSection is used instead of backgroundCorrect
• the boxplotBeads function is removed and the generic boxplot is used for beadLevelData
• imageplot and outlier plot functions include a horizontal to change orientation of the plot to match the orientation of the original TIFF image
• the squareSize parameter is now used to control the resolution of imageplots
• the imageplot function will attempt to read sdf information to determine the optimal values of squareSize
• the checkRegistration function checks for possible errors in the registration of the original image. NB requires locs information to be available.
• the BASH function now returns a QC list item containing the number of masked beads and extended score for each array
• BASH function will accept a transformation function argument instead of 'what'
• control probe annotation for Humanv4 arrays is added to ExpressionControlData
• a 'controlProfile' data frame can be used to make control plots of data which are not defined in ExpressionControlData
• the quickSummary and makeQCTable functions are added to summarize various control types on specified arrays
• the controlProbeDetection function returns the percentage of beads belong to defined set of control types that are expressed above background
• the calculateOutlierStats function returns the percentage of outliers that occur in each segment of a particular array
• the expressionQCPipeline function replaces calculateBeadLevelScores
• 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
• 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.
• 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.
• different summarization schemes are supported in the summarize function, in which case an ExpressionSetIllumina that incorporates the concept of channels will be created.
• the readBeadSummaryData functions will read extra annotation columns from BeadStudio output
• the NoBeads slot in ExpressionSetIllumina has been re-named to nObservations
• 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
• support for neqc (limma) and rsn (lumi) in normaliseIllumina