------------------------- affylmGUI ChangeLog -------------------------
8-Apr-2010 affylmGUI 1.21.0
	fixed documentation bug relating to Filename argument in the openLimmaFile function
	This version ready for release with Bioconductor 2.6 due on April 23 2010

15-Oct-2008 affylmGUI 1.15.1
	[bug]change cdf to cdfName in OpenCDFFile function
	[bug]change arguments call to function ViewContrastsMatrixInTable from
	 (contrastsMatrix,contrastsList,contrastParameterizationIndex) to
	 (contrastsList,contrastParameterizationIndex)
	[bugs]In runOverall function,
 	include "Require("tkrplot") under runType!="runTestOnly" condition(first time).
 	replace "tmpEvalRcodeResults" with "tmpEvalRcodeResultsGraph" under runType!="runTestOnly" condition(second time).
	[bug]In chooseCDF function, change "cdfDataFrame" to "cdfPackages" in the onOK function
	Remove gif file type references in htmlReport.R and replace with png type files
	Replace file R2HTMLlogo.gif with R2HTMLlogo.png file.

20-Apr-2008 affylmGUI 1.13.1
	Remove some corrections by P. Aboyoun in main.R. The references to exprSet are needed
	to check old data files for class name of exprSet and if present retrieve data from them
	without needing the exprSet class definition.
	also reformat the layout of some code to my liking.
	Update the text in main.R about not working with Tcl/Tk.
	Changed license to LGPL
	Added LazyLoad: yes to DESCRIPTION file
	This version ready for release with Bioconductor 2.2

21-Sep-2007 affylmGUI 1.11.6
	HTML Report Report uses options for Top Table that are set when TopTable menu choice is used.
	Reformatted code in main.R and htmlReport.R for consistency

13-Sep-2007 affylmGUI 1.11.5
	Display Citation in TckTk GUI message box as well as writing citation to R console

20-Jun-2007 affylmGUI 1.10.4
	References to Digestion changed to Degradation. Changed Menu Item name and function names
	See Bioconductor emails from Gordon Smyth/Robert Gentleman around December 6th. 2006.

	Fixed a bug in Normalize.R introduced in 1.10.1 - bracket misplaced as shown below:
	Replaced this line
		Try(write.table(NormalizedAffyData.exprs),file=FileName,sep="\t",quote=FALSE,col.names=NA)
	with
		Try(write.table(NormalizedAffyData.exprs,file=FileName,sep="\t",quote=FALSE,col.names=NA))

	Error on console when HTML report was to be created. It read:
		"Error in get(x, envir, mode, inherits) : variable "HTMLenv" was not found"
	Modify htmlreport.R
	replace:
		try(assign(".HTML.graph", TRUE, env = get("HTMLenv", envir = .GlobalEnv)))
	with:
		if (exists("HTMLenv",where=".GlobalEnv",mode="environment")){
			try(assign(".HTML.graph", TRUE, env = get("HTMLenv", envir = .GlobalEnv)))
		}#end of if (exists("HTMLenv",where=".GlobalEnv",mode="environment"))

8-Jun-2007 affylmGUI 1.10.3
	Mispelling in main.R. Replace NormalizedAffyDatase.@exprs with NormalizedAffyData@se.exprs

31-May-2007 affylmGUI 1.10.2
	Fix PLM Normalization problems relating to use of exprSet and PLMset
	Change data storage of exprSet NormalizedAffyData to two separate
	matrices "NormalizedAffyData.exprs" and "NormalizedAffyData.se.exprs".
	This requires the reading of earlier versions of saved lma files to
	be processed so that NormalizedAffyData.exprs and NormalizedAffyData.se.exprs
	are extracted from the exprSet NormalizedAffyData and the individual
	matrices constructed.

	Replace tkopen, tkread and tkclose in Evaluate Code in main.R

16-May-2007 affylmGUI 1.10.1
	Fix HeatDiagram File menu so that it can save in PNG/JPEG/PS/PDF formats by adding value
	for limmaDataSetNameText to HeatDiagramPlot function in plot.R

	Fixed bug in IntensityHistogramAll function
	#Replace this line with line below#Try(hist(log2(mm(RawAffyData[,slide])),breaks=100,col="blue",xlab=xLabel,ylab=yLabel,main=plotTitle))
	Try(hist(log2(mm(RawAffyData)),breaks=100,col="blue",xlab=xLabel,ylab=yLabel,main=plotTitle))

	Modified way to access data in AffyBatch objects(RawAffyData), Use accessors for exprs, se.exprs, cdfname etc
	in main.R
		#Replace this line with line below#Try(SlideNamesVec <- colnames(RawAffyData@exprs))
			 Try(SlideNamesVec <- colnames(exprs(RawAffyData)))
	in plot.R
	#Replace this line with line below#Try(R <- log2(RawAffyData@exprs[,slide1]))  # Using cDNA notation (R for one channel/array, G for the other)
		 Try(R <- log2(exprs(RawAffyData)[,slide1]))  # Using cDNA notation (R for one channel/array, G for the other)
	#Replace this line with line below#Try(G <- log2(RawAffyData@exprs[,slide2]))  # Using cDNA notation (R for one channel/array, G for the other)
		 Try(G <- log2(exprs(RawAffyData)[,slide2]))  # Using cDNA notation (R for one channel/array, G for the other)

April 2007
	affylmGUI 1.10.0 released with Bioconductor 2.0/R2.5.0

29 September 2006 affylmGUI 1.7.1
	Add documentation entries to affylmGUI.RD for all arguments of functions
	Modify installation of annotation package code(Plot.R) in HeatDiagramPlot function if(length(geneSymbols)==0)
	Modify installation of annotation package code(Plot.R) in affyPlotMAcontrast function if(length(geneSymbols)==0)
	Modify installation of annotation package code(Plot.R) in LogOddsPlot function if(length(geneSymbols)==0)
	Modify (affylmGUI-menus.txt) by adding (One Slide) to several plot options
	The "Intensity Density Plot" on the  Plot Menu option now calls the function "DensityPlotAll",
		which plots Densities for all slides
	Added the function "DensityPlotAll" to Plot.R which plots all slide's Density plot on the one graph.
	Added the "RNA Digestion Plot" option to the Plot Menu option which calls the function "RNADigestionPlotAll".
	Added the RNADigestionPlotAll function which plots an RNA digestion plot for all slides.
	Added the "NUSE-Normalized Unscaled Std.Errors Plot" Plot Menu option which calls the function "NUSEPlotAll".
	Added the "RLE-Relative Log Expression Plot" Plot Menu option which calls the function "RLEPlotAll".
	Renamed the Image Quality Plot on the Plot Menu to the "Weights pseudo chip Image(s) Plot" which now
		calls the function ImageQualityWeightPlot.
	Added the "Residuals pseudo chip Image(s) Plot" to the Plot menu which now clls the function ImageQualityResidualPlot.
	The NUSE, RLE & Weights pseudo chip Image plots call affyPLM and store the Pset result.
	Added appropriate entries in the affylmGUI.Rd file
	Remove "\usepackage{Sweave}" from affylmGUI.Rnw and extract.Rnw

21 April affylmGUI 1.5.4
	Fixed tkcmd(open,filename...) etc. Used tclopen(filename...)
	similarly for tkcmd(read/close).
	Fixed ALGchangeLog - case wrong in some places
	utility.R not uploaded last time.

10 April 2006 affylmGUI 1.5.4
	Remove dependence on reposTools package in main.R and plot.R
	Replace tkcmd with tcl in about 50 places
	Replacing tkcmd(open...) with tclopen(..., similarly for tkcmd read and close
	  did not work, reverted to deprecated tkcmd syntax - need to sort this out.
	Add additional reference to CITATION text file

17 January 2006 affylmGUI 1.5.3
	Add citation entries for gcrma and rma

30 November 2005 affylmGUI 1.4.3
	Add ChangeLog item to Help Menu - shows 20 lines
	Add the showChangeLog function to main.R
	Add Citations item to Help Menu.
	Add Sentence on Main window telling users about the Citations item
	on the Help Menu.
	Fix limma help function on Help menu.
	Make message for help functions appear in R console rather than as a
	separate tkmessage box.
	Add utility.R to R subdirectory which contains the changeLog
	function and the limmaUsersGuide function.

8 November 2005 affylmGUI 1.4.2
- Add this changelog.txt file to the doc sub-directory of the inst sub-directory.

4 November 2005 affylmGUI 1.4.2
- Include PlotOptions.R in distribution to Bioconductor devel site
- Modify main.R - Adjust Menu box for Top Table was changed to only
  display None, BH, BY and Holm as alternative Adjustment methods
- Modify main.R to include Adjustment method in heading of top table plot

October 2005 14 2005: affylmGUI 1.4.0.
	affylmGUI version upgraded from 1.3 to 1.4.0 for release
	by Bioconductor for release with Bioconductor
	version 1.7 (for release after R 2.2.0)
	Maintainer changed from James Wettenhall to Keith Satterley

September 2005: affylmGUI 1.3.0
	Keith Satterley takes over maintenance of program.

PRE-HISTORY

affylmGUI was developed by James Wettenhall, Gordon Smyth and Ken
Simpson between 2003 and October 2005.

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