1.5.16 - 28 September 2007
 - fixed bug in combine() for ExpressionSetIllumina-class (old reference to reporterInfo removed and method now exported properly).
 - change to C code in calculateBackground (readBeadImages.c) function.  If any of the lowest 5 background pixels are saturated, set background to zero, rather than take the average.
 - fixed bug in assignment of pData in readIllumina() when 'targets' have been specified.

1.5.15 - 27 September 2007
 - updated and renamed pdfs which provide example bead-level (beadlevel.pdf) and summary (beadsummary.pdf) analyses.

Version 1.5.14 - 24 September 2007
 - fixed bug in C code in calculateBackground (readBeadImages.c) function (was over-running end of array).  Also made backgroudSize adaptive (was set to fixed size of 17x17 pixels in C code) and is more careful when at an edge (previously set background to 700 if pixels went off the edge).
 - fixed bug in findAllOutliers() (introduced in 1.5.11 when && and || added to if statements.  Inadvertantly added to which at the end of findAllOutliers()) 
 - fixed bug in SAMSummary() BeadChipSummary() - couldn't handle negative summary values and removed unknown 'v' variable assigned when missing_arrays argument was specified.  Removed missing_arrays argument, and added arguments 'samID', 'chipID' and 'stripsPerChip' to allow user to choose which SAM/BeadChip to plot and specify the correct number of strips per chip.  Function is more careful about plotting the data in the appropriate row/column position, and returns a message it the user clicks out of range.  Missing arrays are coloured white.
- removed unknown 'v' variable assigned when missing_arrays argument was specified in plotOnSAM().
- getArrayData() now checks for out of range or NA 'array' argument and returns a message
- createBeadSummaryData() checks for arraynm in full list of array names in case 'array' has not been specified as an integer.

Version 1.5.13 - 20 September 2007
 - example BLData.rda object in package updated

Version 1.5.12 - 18 September 2007
 - phenoData in BLData object created by readIllumina() contains 1 column 'arrayName' when no targets information is set.
 - example BLData.rda object in package updated with phenoData information.

Version 1.5.11 - 17 September 2007
 - removed returnTIFF.c (not used anymore).
 - NAs or Infs in imageplot() and createBeadSummaryData() now excluded (previously set to zero).
 - log2.na() (not exported) used in getArrayData() to avoid throwing up a
 warning message when 0's or negative values are log2.
 - when useImages=FALSE in readIllumina(), x-, y-coordinates read from file are
 now adjusted to start at 0,0 (useful for image plotting).
 - readBeadSummaryData() has new argument  ... to take additional
 arguments to read.table (quote="", fill=TRUE sometimes needed for BeadStudio
 3 data). Reverses changes to readBeadSummaryData made in 1.5.10 and 1.5.7.
 - new argument 'legend' in imageplot() to display range and zlim on plot.
 - new argument 'arrays' in arrayNames() to get the name of a selected array/s.
 - new function getVariance() returns the variance for each bead-type on each
 array from an ExpressionSetIllumina object (calculated from se.exprs and
 NoBeads slots).
 - SnpSetIllumina doesn't store se.exprs for each channel - removed code
 which assigns the se.exprs to a SnpSetIllumina object in
 createBeadSummaryData()
 - fixed broken link in BSData.Rd help page.
 - default annoPkg argument in readIllumina() is "illuminaProbeIDs" (not actually an annotation package, but is there to tell the user that ProbeIDs are used to identify each bead type (not Illumina IDs available in existing annotation packages)
 - createBeadSummaryData(): The phenoData slot is set to have 1 column 'sampleName' which is set to the array names if no phenoData information has been set.  sampleNames are set to either the 'sampleName' from phenoData, or the array names.

Version 1.5.10 - 3 September 2007
 - added new options to createBeadSummaryData (see "method" and "trim"
 arguments) to allow mean, median, trimmed mean or winsorized means to 
 be calculated to summarise the values from each beat type on an array.  
 createBeadSummaryData.c code edited to allow new options
 - "which" argument changed to "what" in getArrayData().  Also added new
 arguments ("method" and "trim") for use by createBeadSummaryData when 
 what="residG", "residR" or "residM" to allow control over summarisation 
 methods. Updated arguments of getArrayData() when called in other bead 
 level plotting functions.
 - Added new arguments to boxplotBeads, imageplot, plotBeadDensities, etc 
 to accept these new arguments to getArrayData (when whatToPlot="residG", 
 "residR" or "residM")
 - added FILL=TRUE to read.table() used in readBeadSummaryData() in response
 to message on BioC list from Ina Hoeschele about error trying to read in 
 BeadStudio version 3 data caused by line having incorrect number of entries
 - updated help pages

Version 1.5.9 - 1 August 2007
 - changed default quote argument in readBGX() to quote="" (i.e. disabled)
 - updated readBGX() man page

Version 1.5.8 - 31 July 2007
 - normaliseIllumina.RD added
 - spelling mistake in message in readIllumina() corrected
 - corrected plot orientation and setting of zlims in imageplot()
 - corrected plot orientation in plotBeadLocations()
 - createBeadSummaryData() NA or Inf values replaced by 0 when log=TRUE/FALSE (previously only occurred when log=TRUE)
 - plotBeadDensities() now allows different colours for each channel plotted

Version 1.5.7 - 23 July 2007
 - normaliseIllumina, offers normalisation for ExpressionSetIllumina objects
 - readBeadSummaryData, default options changed to handle BeadStudio 3 output (skip=8, added 'quote=""' to read.table (default 'quote'
 caused R to hang for some BeadStudio version 3 output))
 sep arguments to be correct for version 3 outputetc.)
 - vsn2 used in normalizeSingleArray, instead of vsn
 - displayTIFFImage and plotCoord removed
 - plotMA and plotXY updated to now check for and exclude missing values from plotting
 - createBeadSummaryData now checks that the arrays it combines (when 'imagesPerArray=2') are the right ones.  New argument 'what', which allows log-ratios (M), average intensites (A), red (R), green (G) or red and green (RG) intensities to be summarised.  Default 'imagesPerArray' set to 1 instead of 2.
 - getArrayData:  typos in error messages fixed.  New 'which' option 'residM'
 top get residuls from log-ratios.
 - readIllumina: default background correction option changed to 'subtract'
 - imageplot: changed default nrow and ncol to 100 (was 18 and 2 respectively)
 - beadResids() simplified after changes to getArrayData
 - updated man pages

Version 1.3.1 - 12 Feb 2007

BeadLevelList
 - changed structure to accommodate varying numbers of beads per array
 - new slots 'beadData' (environment) which stores raw data in data.frames,
 one for each array, 'phenoData' (AnnotatedDataFrame) to store targets/sample 
 information, 'arrayInfo' (list) which stores array names, number of beads 
 and other array information, and 'scanMetrics' which stores scanner setting 
 information
 - updated plotting functions to handle data in new structure
 - updated createBeadSummaryData to handle new structure

New functions
 - plotRG, for two-colour data
 - boxplotBeads, to do boxplots of the raw intensities
 - getArrayData, numBeads, arrayNames for use on BeadLevelList data

Changes to C code
 - commented out 'bead is too close to edge, ignoring' warning in readBeadimages
 - changed default setting of BLImagePlot to take log2 of the data passed to it
 - findAllOutliers now takes 'nmads' argument to select outliers
 - createBeadSummary also accepts 'nmads'

Data
 - new BLData object (4 arrays from a SAM)
