2014-11-24: 1.08-3

	. Changed package title to title case in description and help files.

2014-11-24: 1.08-2

	. Removed the junk file 'support' from the toplevel directory.

2009-10-11: 1.08-1

	. fix help file for consensusMEDissimilarity

2008-06-11: 1.08

	. multiSetMEs gains the argument useGenes that can optionally specify a subset of genes to be
	  used for calculations.

2008-05-16: 1.06-1

	. One more fix for plotHclustColors: now correctly uses names of given colors, if they
	  exists. 

2008-05-10: 1.06

	. saving and restoring of the random number seed in moduleEigengenes 
	  now works correctly.

	. plotHclustColors now correctly uses names of given colors, if they
	  exists.
	
	. mergeCloseModules can now optionally exclude grey ME from being calculated (faster
	  and less uninteresting output). Set getNewGreyME = FALSE to exclude the grey ME. 
	  The default is TRUE for backward compatibility.

	. orderMEs now correctly orders varExplained as well

	. Fixed a bug in mergeCloseModules which caused the names of
	  calculated MEs to correspond to labels before relabeling.

	. Corrected a problem in hub calculation that caused the returning of
	  unnecessary NAs in moduleEigengenes

2008-04-09: 1.05-03

	. Changed calculation of proportion of variance explained in
	  moduleEigengenes. The calculation is now exact irrespective of nPC.
	  The argument nPC now only serves to indicate how many varExplained
	  entries are desired.
	. Added argument impute = TRUE to mergeCloseModules that gets passed
	  to multiSetMEs. 
	. removed a bug in mergeCloseModules that caused failure with one
	  proper module and relabel = TRUE
	. removeGreyME now works also when MEs is a matrix (previously worked
	  only when MEs was a data frame). 

2008-04-03: 1.05-02

	. Bugfixes: misspelled variables and misplaced brackets

2008-04-01:

	. Minor improvements in precision of color alignment in plotHclustColors 

2008-03-26: 1.05-1

	. bugfix: mergeCloseModules behaves properly when input 'colors' is a factor, 
	in particular it drops unused levels to avoid returning empty modules.

2008-03-12: 1.05

	. error trapping in moduleEigengenes revised: hubs can be substituted
	for eigengenes whose calculation failed.

	. mergeCloseModules gets its own trapErrors, but it isn't all that
	useful right now.


2008-03-07: 1.04-01

	. bugfixes in multiSetMEs

2008-03-06: 1.04

	. moduleEigengenes and multiSetMEs now optionally trap errors in module
	eigengene calculation and remove the offending modules from the
	result.

	. moduleEigengenes and multiSetMEs can optionally exclude the grey
	module eigengene from the returned PCs.

	. moduleEigengenes and multiSetMEs can optionally return only the
	valid PCs

(2008-03-03)

	colors2labels checks for NAs in labels

2008-02-27

	1.03-04: colors2labels: return value now has the dimensions of input
	labels, so works correctly on matrices and such.

2008-02-24

	1.03-03: changing default MEprefix to "ME". setMEprefix doesn't seem to work!

2008-02-20

	mergeCloseModules: all print statements are printFlush for consistency.

2008-02-16:
	plotHclustColors now uses names(colors) as rowNames if the latter are NULL and the former
	are valid (have the right lenght).

2008-02-14:
	Fixed a couple of bugs in .clustOrder. 

2008-02-12:
	Fixed problems in mergeCloseModules, consensusOrderMEs, orderMEs when
	number of proper modules is 1 or none.  

2008-02-05:
	Fixed error in removeGreyME.

2008-01-31:
	Added the function removeGreyME

2008-01-29: Version 1.03: 
	Minor robustness improvements: 
	 . mergeCloseModules won't fail if there are less than two proper modules.
	Addition of options:
	 . moduleColor.[set,get]MEprefix: the prefix used to label module
	 eigengenes. For compatibility with old code, standard startup value
	 is "PC", but recommended value is "ME".

2008-01-24: Minor bug fixes:
	Make the call to impute.knn more crash-resistant: The parameter k now doesn't exceed 
	number of supplied genes -1.
	White was listed twice in BaseColors; second instance removed (thanks
	to Jeremy Miller for noticing this)

2007-11-21: Functionality improvement/bug fix:

	checkSets: now accepts parameter useSets to only check selected
	components of the data vector. This fixes a problem with calling
	consensusOrderMEs, mergeCloseModules etc. with multi-data but only for
	one set.

2007-09-18: version: 1.02

	mergeCloseModules: changed default useAbs to FALSE (!!!!)
	                   fixed a bug in counting of old and new modules
			   fixed a bug appearing when no merging was necessary
			   
	plotHclustColors, moduleEigengenes: color changed to colors (!)

	moduleEigengenes: Decreased verbosity for verbose=1

	orderMEs: grey ME not found triggers a warning instead of an error.

	labels2colors: if number of labels exceeds number of availbale colors,
	recycle colors with suffix .1, .2 etc added. Caution: this will make
	extra colors incompatible with standard plotting, but compatible with
	mergeCloseModules (which relies on names of different modules being
	unique).

	normalizeLabels: fixed a bug that merged modules of same size because
			rank was resolving ties by averages.


2007-09-17: version 1.01.01

Bug fixes and small changes:

	moduleEigengenes: fixed problem with saving .Random.seed if the variable doesn't exist (yet)

	multiSetMEs: added argument impute

	plotHclustColors: Fixed to work if color is a single vector of colors

	updated URL in DESCRIPTION