CHANGES IN VERSION 2.1.3
-------------------------
- fix the groupComparison for label-free experiments.
- automatically generate progress report as .txt files
- add progress message for groupComparison and dataProcessPlots function.


CHANGES IN VERSION 2.1.1
-------------------------
- fix the bug in Condition plot : 
	1. for label-based : match reference and endogenous
	2. for label-free : when there is one observation in each group, SD=NA. make it zero.
- fix the bug in heatmap and comparison plots : remove NA result for plotting
- fix the bug for label-free groupComparison :  how to get subject_nested parameter in make.contrast.free for unequal number per group
- fix the bug in group quantification : make.contrast.group.quantification fixed for subject_nested parameter


CHANGES IN VERSION 1.99.1
-------------------------
- fixed several NOTES, added .Rbuildignore, compacted vignettes
- TODO: check remaining 'no visible binding for global variable' NOTES
- removed warn -1 
- added validity check when returning MSnSet
- used inherits/is. for class testing
- TODO fix if conditions syntax

CHANGES IN VERSION 1.99.0
-------------------------
 o improve efficiency for computing groupComparison and quantification <2012-12-21>
 o add .rnw <2012-12-03>
 o update groupComparision for label-free time-course experiment with single Feature and with or without technical replicates <2013-04-08>
 o add option for saving QQ plot and Residual plot in order to checkin the normality assumption in groupComparison function. <2013-04-08>
 o use ggplot2 package for all plots. <2013-07-11>
 o fix bug for volcano plot : different color labeling <2013-07-12>
 o add power plot in sample size calculation plot <2013-07-12>
 o add 'interference=TRUE or FALSE' in sample size calculation <2013-07-15>
 o add 'legend.size=7'for size of feature name legends in dataProcessPlots <2013-07-23> 
 o add 'text.angle=0'for angle of condition labeling in dataProcessPlots <2013-07-23>
 o fix bug for quantification : when there are missing values in endogenous intensities, but values in reference intensities. <2013-07-24>
 o fix bug for groupComparison : when there are missing values in endogenous intensities, but values in reference intensities, .make.constast.based or .free sub function were changed. <2013-07-25>

o two function for transformation between required input for MSstats and MSnSet class <2013-09-04>
o flexibility for visualization : save as pdf files or show in window with selected proteins or all proteins. <2013-09-04>
o handle unequal variance for feature in groupComparison function with featureVar=TRUE <2013-09-04>

o Add 'missing.action' for impute missing values in group comparison stage. <2013-09-20>











