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)

