Changes in version 1.10:

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    o   Using NEWS.Rd

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    o   batch slot in CNSet objects is class 'character' (previously, class
	was 'factor')

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    o   the ff package is required for preprocessing and genotyping prior
	to copy number analyses with the crlmmCopynumber function.

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    o   We have added several vignettes pertaining to copy number analyses
	in the crlmm package: CopyNumberOverview, AffymetrixPreprocessCN,
	IlluminaPreprocessCN, and Infrastructure.  The
	AffymetrixPreprocessCN and IlluminaPreprocessCN vignettes provide
	instructions for preprocessing and genotyping the raw intensities
	for Affymetrix and Illumina platforms, respectively.  The
	'copynumber' and 'Infrastructure' vignettes are applicable to both
	the Illumina and Affymetrix platforms. The CopyNumberOverview
	vignette provides a brief summary of the available vignettes for
	copy number analysis.

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    o   For those interested in copy number analysis of Illumina platforms,
	we added functions that break-down the preprocessing and genotyping
	steps: constructInf, preprocessInf, and genotypeInf. The
	genotype.Illumina function is now a wrapper for these functions.

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    o   additional documentation for crlmm is provided in a compendium:
	http://www.biostat.jhsph.edu/~rscharpf/crlmmCompendium/index.html

Changes in version 1.8:

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    o   define CNSet class with batch and batchStatistics slots

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    o   deprecate CNSetList class

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    o   deprecate crlmmWrapper, genotype2, and crlmmCopynumber2.  Use
	crlmmCopynumber in place of crlmmWrapper and crlmmCopynumber2.  Use
	genotype instead of genotype2.

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    o   raw copy number estimates no longer stored in container.  CA and CB
	methods are no longer simple accessors to data stored in the
	eset-extension.  These functions compute raw copy number estimates
	from the linear model parameters.

Changes in version 1.3:

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    o   3 new classes created:
	
	  * 'ABset': container for quantile-normalized A and B intensities
	    for both SNP and copy number probes.  Required assay data
	    elements are 'A' and 'B'.  Extends eSet directly.
	
	     1. For nonpolymorphic probes, the quantile normalized
	        intensity is stored in the 'A' assay data element.  The
	        corresponding row in the 'B' assay data element is NA.
	        This is a bit inefficient, but greatly simplifies
	        downstream analyses.  In particular, '[' works.
	
	  * 'CrlmmSetList': container for results from preprocessing and
	    genotyping.  This object is a list.  The first element of the
	    list is an ABset.  The second element is a SnpSet containing
	    genotype calls.  The two elements are required to have
	    identical featureNames and sampleNames.
	
	     1. added several methods for subsetting and accessing elements
	        of this object, including featureNames, sampleNames, and
	        '['.
	
	  * 'CopyNumberSet': contains locus-level estimates of copy number
	    for SNPs and polymorphic probes.
	
	     1. Required assay data elements are 'CA' and 'CB',
	        corresponding to the absolute copy number for allele A and
	        B, respectively.
	
	     2. For nonpolymorphic probes, the total copy number is stored
	        in the 'CA' slot and a NA is recorded for the corresponding
	        row in the CB matrix.
	
	     3. Useful methods: 'copyNumber', 'ellipse', 'points'

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    o   'crlmmWrapper' function does preprocessing (quantile-normalization)
	and genotyping, saving an object of class CrlmmSetList for each
	chromosome

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    o   'computeCopynumber' now requires an object of class 'CrlmmSetList'
	and returns an object of class 'CopyNumberSet'.