v1.3.13
- Moved gtools from Suggests to Imports
- Removed multiple instance of 'f' function in ExpressionSetList[ method

v1.5.3
- Corrected bug in zeroNu function (needed to pass one.delta argument
  to empiricalStart function)
- fixed bug in reading acceptance  and potential for XdeMCMC objects

v1.5.4
- added burnin argument to calculatePosteriorAvg function

v1.5.5 6/4/2009
- For parameters indexed by genes and platforms, the chains were read in incorrectly
	## - The order of the vector for parameter nu_gp indexed by gene g and study p is
	##     nu_11, nu_12, ..., nu_1P, nu_21, ..., nu_2P, nu_G1, ..., nu_GP
	##
	## Arrays:  the 'left subscript moves the fastest'
	##Therefore
	##  mcmc <- array(mcmc, dim=c(# iterations, # genes, # studies)) is equiv to
	## For iteration 1:
	## mcmc[1, 1, 1] <- nu_11
	## mcmc[1, 1, 2] <- nu_12
	## mcmc[1, 1, P] <- nu_1P
	## mcmc[1, 2, 1] <- nu_21
	## mcmc[1, 2, P] <- nu_2P

v1.5.6 6/4/2009
- Fixed bugs in functions calculatePosteriorAvg and calculateBayesianEffectSize

v1.5.7 6/4/2009
- The chains were actually read in correctly prior to v.1.5.5.
   Changes the comments below in methods-XdeMcmc.

- Note that we're returning aperm(mcmc) for parameters indexed by
   genes and platforms, so the changes in "bug" fix 1.5.6 still work

	##---------------------------------------------------------------------------
	##Parameters indexed by gene and study
	##
	## If ITER iterations were executed, there are ITER lines written to the file. 
	## Each line is a big vector in the following order:
	## gene1 study 1, gene 1 study2, ... , gene1 study P, gene 2 study 1, ...
	## Or,
	##iter1:     nu_11, nu_12, ..., nu_1P, nu_21, ..., nu_2P, nu_G1, ..., nu_GP
	##iter2:     nu_11, nu_12, ..., nu_1P, nu_21, ..., nu_2P, nu_G1, ..., nu_GP
	##
	## for the nu parameter.
	##
	## For reading in arrays, the 'left subscript moves the fastest'
	##
	## scan() reads in the data by rows.
	## Therefore, the fastest moving index is study, followed by genes and then the mcmc iteration. 
	##
	##  mcmc <- array(mcmc, dim=c(# studies, # genes, # iterations)) is equiv to
	## For iteration 1:
	## mcmc[1, 1, 1] <- nu_11
	## mcmc[2, 1, 1] <- nu_12
	## mcmc[P, 1, 1] <- nu_1P
	## mcmc[1, 2, 1] <- nu_21
	## mcmc[2, 2, 1] <- nu_22
	## ...
	## mcmc[P, 2, 1] <- nu_2P
	## ...
	##---------------------------------------------------------------------------	
	if(name %in% c("DDelta", "nu", "phi", "sigma2", "delta", "probDelta")){
		I <- iterations(x)
		mcmc <- array(mcmc,
			      dim=length(studyNames(x),
			      nrow(x),
			      iterations(x)),
			      dimnames=list(studyNames(x),
			      featureNames(x),
			      as.character(1:I)))
		##Now transform this to an array with dimensions:
		## iteration x features x study
		mcmc <- aperm(mcmc)
		return(mcmc)
	}
	##--------------------------------------------------

v 1.5.8 Fixed bug in converting the mcmc object to an array

v 1.5.9 committed 6/22/2009
  o updated the elements of expressionSetList -- elements now have scanDates() slots
  o fixed documentation errors

v 1.5.10 committed 6/25/2009
  o fix warning:  added seed to XdeParameter-class man page 


v 1.5.11 committed 7/23/2009
  o updated the elements of expressionSetList -- elements now have
    protocolData slots


v 1.5.12 committed 8/10/2009
  o try to fix compile errors on gewurz: option authoryear and natbib
    not working. Trying:
        \usepackage[authoryear,round,numbers]{natbib} 

  o added seed to man/XdeParameter-class slots
  o updated vignettes / pdf
  o added NEWS file

v 1.5.13 committed 9/29/2009
  o removed authoryear option from natbib in Sweave fileg

v 1.5.14 committed 10/02/2009
  o removed debugging code from xde.R

v 1.5.15 committed 10/02/2009
  o resurrected old copy of xde.R

v 1.7.1 committed 12/04/2009
  o  added integrativeCorrelationFilter
       - returns a TRUE/FALSE matrix for each gene x study-pair
  o import MergeMaid

v 1.9.1 committed 05/18/2010
  o changed empiricalStart function so that it is possible to use
  empirical values for a single study
