CHANGES IN VERSION 1.2.1
-------------------------


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 1.2.0
-------------------------


SIGNIFICANT USER-VISIBLE CHANGES

    o None, just updating version to be consistent with release
    

BUG FIXES AND MINOR IMPROVEMENTS

    o None


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