Changes in version 1.10                         

USER VISIBLE CHANGES

    o   Using NEWS.Rd

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

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

    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.

    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.

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

                         Changes in version 1.8                         

USER VISIBLE CHANGES

    o   define CNSet class with batch and batchStatistics slots

    o   deprecate CNSetList class

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

    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                         

USER VISIBLE CHANGES

    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'

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

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