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        *                                                *
        *              1.5 SERIES NEWS                   *
        *                                                *
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USER VISIBLE CHANGES

NEW FEATURES

	o Support to large datasets via ff package. The user
	must load the ff package manually to benefit from
	this.

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        *                                                *
        *              1.3 SERIES NEWS                   *
        *                                                *
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USER VISIBLE CHANGES

     o 3 new classes created:

        i.  '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.

                - 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.

        ii.  '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.

       		- added several methods for subsetting and accessing
 		  elements of this object, including featureNames,
 		  sampleNames, and "[".

         iii. 'CopyNumberSet': contains locus-level estimates of copy
  	      number for SNPs and polymorphic probes.

       	        - Required assay data elements are 'CA' and 'CB',
                  corresponding to the absolute copy number for allele
                  A and B, respectively.

	        - 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. 

		- 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'.