CHANGES IN VERSION 1.13.1
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES
    o replaced QuasiSeq with edgeR for differential expression testing, due to deprecation of QuasiSeq
    o users will observe significant speed increases for DE testing
    o users will observe changes in results from example data, Quasi-Likelihood methods are similar for edgeR and QuasiSeq, but not exactly identical, so P-value distributions are different, LODR estimates have changed.
    o dispersion plot (dispPlot) is now generated via edgeR instead of QuasiSeq, using a similar Quasi-Likelihood dispersion shrinkage method.
    
    
BUG FIXES AND MINOR IMPROVEMENTS
    o changed behavior so that dispPlot is not deleted if DE testing is rerun, instead increment file name to prevent overwriting.


CHANGES IN VERSION 1.7.2
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES
    o 
    
BUG FIXES AND MINOR IMPROVEMENTS
    o Fixed minor syntax issues in Rd files
    o Added more importFrom calls to Namespace file

CHANGES IN VERSION 1.7.1
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES
    o 
    
BUG FIXES AND MINOR IMPROVEMENTS
    o Fixed conditional statement for normalized microarray data in testDEArray.
    o Added dev.off to close the last plot in an attempt to prevent Rplots.pdf 
    when run via Rscripts on commandline.


CHANGES IN VERSION 1.5.1
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES
    o 
    
BUG FIXES AND MINOR IMPROVEMENTS
    o simplified normalizeDat function, since array data and count data are 
    treated the same, if repNormFactor (normalization factors) isn't provided 
    by the user, then 75th percentile normalization is used. 10^6 multiplier 
    that was used for per million read scaling is removed for the case of user 
    provided repNormFactor (it's unlikely that this was used by most users)
    
    o removed deprecated calls from ggplot2 (show_guide --> show.legend)


CHANGES IN VERSION 1.3.5
-------------------------


SIGNIFICANT USER-VISIBLE CHANGES
    o Updated help files
    
BUG FIXES AND MINOR IMPROVEMENTS

    o add warning if sample1Name or sample2Name include spaces or special characters.

CHANGES IN VERSION 1.3.4
-------------------------


SIGNIFICANT USER-VISIBLE CHANGES


    o None

BUG FIXES AND MINOR IMPROVEMENTS

    o Fixed allReps and labelReps value assignment

    o Fixed bug for duplicate row names in array data
    
    o Fixed warning for incorrect sample names


CHANGES IN VERSION 1.3.3
-------------------------


SIGNIFICANT USER-VISIBLE CHANGES


    o Updated dynRangePlot - function can now plot all replicates with or 
        without replicate labels

BUG FIXES AND MINOR IMPROVEMENTS

    o Added warnings to initDat function for incorrect sample names and missing
        1:1 controls from userMixFileß
    o Set minimum version requirements for ggplot2 and gridExtra
    

CHANGES IN VERSION 1.3.2
-------------------------


SIGNIFICANT USER-VISIBLE CHANGES


    o Vignette is updated to include use of grid.arrange for viewing figures
    
    o multiplot function is deprecated and removed from the package, 
        function is replaced with grid.arrange
    

BUG FIXES AND MINOR IMPROVEMENTS

    o updated erccROC, estLODR, and maSignal to address changes to tableGrob in 
        gridExtra package
    

CHANGES IN VERSION 1.3.1
-------------------------


SIGNIFICANT USER-VISIBLE CHANGES


    o Version incremented to 1.3.1 for development.

BUG FIXES AND MINOR IMPROVEMENTS

    o Updated DESCRIPTION file, NEWS file and .gitignore file


CHANGES IN VERSION 1.1.1
-------------------------


SIGNIFICANT USER-VISIBLE CHANGES


    o Version incremented to 1.1.0 for Bioconductor 3.1 release.

BUG FIXES AND MINOR IMPROVEMENTS

    o Updated NEWS file, DESCRIPTION file,and improved documentation in vignette.


CHANGES IN VERSION 1.0.0
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Version set to 1.0.0 for Bioconductor 3.0 release.
    o No updates from 0.99.4.


CHANGES IN VERSION 0.99.4
-------------------------


BUG FIXES AND MINOR IMPROVEMENTS

    o Updated saveERCCPlots, description file, and citation file.



CHANGES IN VERSION 0.99.1
-------------------------


BUG FIXES AND MINOR IMPROVEMENTS

    o Fixed bug in erccROC and estLODR code to only use P-values from ERCCs by coding 
    "ERCC-00" prefix instead of "ERCC-" which in some cases might find endogenous
    transcripts named with this prefix.



CHANGES IN VERSION 0.99.0
-------------------------

NEW FEATURES

    o Version set to 0.99.0 for submission to Bioconductor

ISSUES

    o CMD check still takes too long (> 5 minutes), probably due to differential 
    expression testing in underlying package. This will be difficult to change.


CHANGES IN VERSION 0.9.12
-------------------------

BUG FIXES AND MINOR IMPROVEMENTS

    o Shortened vignette to reduce installation time 

    o Fixed userMixFile as.factor bug

    o Updated namespace to pull in mgcv and nlme package functionality


ISSUES

    o CMD check still takes too long (> 5 minutes), probably due to differential 
      expression testing in underlying package. This will be difficult to change.

CHANGES IN VERSION 0.9.11
-------------------------

BUG FIXES AND MINOR IMPROVEMENTS

    o Added examples to several functions including "dontrun" to minimize
      installation time

    o Updated Namespace to include gplots


