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* 						Changes in version 0.3							*
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NEW FEATURES

	o Now requires R 2.10
	
	o New list slot 'misc' in class 'NMF' to be able to define new NMF models, 
	without having to extend the S4 class. Access is done by methods '$' and '$<-'.
	
	o More robust and convenient interface 'nmf'
	
	o New built-in algorithm : PE-NMF [Zhang (2008)]
	
	o The vignette and documentation have been enriched with more examples and 
	details on the functionalities.
	
	o When possible the computation is run in parallel on all the available cores.
	See option 'p' or 'parallel=TRUE' in argument '.options' of function 'nmf'.
	
	o Algorithms have been optimized and run faster
	
	o Plot for rank estimation: quality measure curves can be plotted together 
	with a set of reference measures.
	The reference measures could for example come from the rank estimation of 
	randomized data, to investigate overfitting.
	
	o New methods '$' and '$<-' to access slot 'extra' in class 'NMFfit'
	These methods replace method 'extra' that is now defunct.
	
	o Function 'randomize' allows to randomise a target matrix or 
	'ExpressionSet' by permuting the entries within each columns using a
	different permutation for each column. It is useful when checking for
	over-fitting. 
		
CHANGES

	o The 'random' method of class 'NMF' is renamed 'rnmf', but is still 
	accessible through name 'random' via the 'seed' argument in the 
	interface method 'nmf'. 
	
NEWLY DEFUNCT CLASSES, METHODS, FUNCTIONS, DATA SETS

    o Defunct Generics/Methods
       1) 'extra' - S4 generic/methods remains with .Defunct message.
       It will be completely removed from the package in the next version.

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* 						Changes in version 0.2.4						*
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CHANGES
	
	o Class 'NMFStrategy' has a new slot 'mixed', that specify if the algorithm 
	can handle mixed signed input matrices.
	
	o Method 'nmf-matrix,numeric,function' accepts a new parameter 'mixed' to 
	specify if the custom algorithm can handle mixed signed input matrices.

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* 						Changes in version 0.2.3						*
*************************************************************************

NEW FEATURES

    o Package 'Biobase' is not required anymore, and only suggested.
    The definition and export of the NMF-BioConductor layer is done at 
    loading.

    o 'nmfApply' S4 generic/method: a 'apply'-like method for objects of 
    class 'NMF'.
    
    o 'predict' S4 method for objects of class 'NMF': the method replace the now
    deprecated 'clusters' method.
    
    o 'featureNames' and 'sampleNames' S4 method for objects of class 'NMFSet'.
    
    o sub-setting S4 method '[' for objects of class 'NMF': row subsets are 
    applied to the rows of the basis matrix, column subsets are applied to 
    the columns of the mixture coefficient matrix.

CHANGES
	
	o method 'featureScore' has a new argument 'method' to allow choosing between 
	different scoring schema.
	
	o method 'extractFeatures' has two new arguments: 'method' allows choosing 
	between different scoring and selection methods; 'format' allows to specify 
	the output format.
	NOTE: the default output format has changed. The default result is now a 
	list whose elements are integer vectors (one per basis component) that 
	contain the indices of the basis-specific features. It is in practice what 
	one is usually interested in.  

BUG FIXES

    o Methods 'basis<-' and 'coef<-' were not exported by file NAMESPACE.
    
    o Method 'featureNames' was returning the column names of the mixture 
    coefficient matrix, instead of the row names of the basis matrix.
    
    o 'metaHeatmap' with argument 'class' set would throw an error.

NEWLY DEPRECATED CLASSES, METHODS, FUNCTIONS, DATA SETS

    o Deprecated Generics/Methods
       1) clusters - S4 generic/methods remain with .Deprecated message
