Changes in version 1.4.2:

    o   Change contact emails; bugfixes and warnings.

Changes in version 1.4.1:

    o   Bugfixes and warnings.

Changes in version 1.4.0:

    o   Plotting
	
	  * dba.plotMA
	
	      * Smooth plots now default
	
	      * Added fold parameter in addition to th (threshold)
	
	  * dba.plotHeatmap
	
	      * Side colorbars added
	
	      * Add support for specifying sample mask to include any
	        subset of samples in a contrast plot, including samples
	        that were not in the original contrast
	
	  * dba.plotVenn
	
	      * Changed plotter from limma to T. Girke's overLapper
	
	      * Added support for 4-way Venns (also in dba/overlap)
	
	  * dba.plotPCA
	
	      * Add support for specifying sample mask to include any
	        subset of samples in a contrast plot, including samples
	        that were not in the original contrast

    o   Peaksets (dba and dba.peakset)
	
	  * Peakset formats
	
	      * narrowPeaks format supported
	
	      * Can override file format, score column, and score
	        orientation defaults for supported peak callers
	
	  * Consensus peaksets
	
	      * Added ability to generate sets of consensus peaksets based
	        on metadata attributes: for example create consensus
	        peaksets for each tissue type and/or condition, or for all
	        unique samples by taking the consensus of their replicate
	        peaksets

    o   Read counting (dba.count)
	
	  * Compute Signal-to-Noise ratio when counting
	
	  * Added bScaleControl to down-scale control reads by default
	
	  * Add option to specify a mask in peak parameter to limit which
	    peaksets are used to for a consensus by overlap. Works with new
	    consensus peakset options in dba.peakset
	
	  * Remove references to support for SAM files

    o   Analysis (dba.analyze)
	
	  * edgeR: updated calls to math change sin edgeR; updated vignette
	    and references
	
	  * DESeq: updated to work with current DESeq; use pooled-CR
	    dispersion estimation method for blocking analysis; update
	    vignette

    o   Various bug fixes; more informative warnings; update documentation
	including vignette, new examples and cross-referencing in man pages

Changes in version 1.2.3 (2012-09-01):

    o   more informative warnings and minor bug fixes.

Changes in version 1.2.0 (2012-03-30):

    o   GRanges is default class for peaksets and reports instead of
	RangedData, controlled by DataType parameter.

    o   Both analysis methods (edgeR and DESeq) use generalized linear
	models (GLMs) for two-group contrasts by default.

    o   Blocking factors (for two-factor analysis) can be specified
	flexibly such that arbitrary blocking factors can be used.

    o   Section added to vignette showing an ananalysis using a blocking
	factor.

    o   Added new metadata type, DBA_TREATMENT.

    o   New DBA_SCORE_ options for specifying scoring method, including TMM
	normalized counts, and ability to change scoring method on the fly
	in dba.plotHeatmap and dba.plotPCA when plotting global binding
	matrix.

    o   bRemoveDuplicates parameter in dba.count allows duplicate reads to
	be discarded when computing counts

    o   More efficient use of memory when analyzing (controlled by
	bReduceObjects parameter in dba.analyze).

    o   various bugs fixed, man pages updated, and warning messages added.