\HeaderA{limmaGUI}{Graphical User Interface for the limma microarray package}{limmaGUI}
\aliasA{AboutCustomMenu}{limmaGUI}{AboutCustomMenu}
\aliasA{AboutLimmaGUI}{limmaGUI}{AboutLimmaGUI}
\aliasA{AboutNormalization}{limmaGUI}{AboutNormalization}
\aliasA{addMenuItem}{limmaGUI}{addMenuItem}
\aliasA{BChelp}{limmaGUI}{BChelp}
\aliasA{ChooseContrastsParameterization}{limmaGUI}{ChooseContrastsParameterization}
\aliasA{chooseDir}{limmaGUI}{chooseDir}
\aliasA{ChooseEbayesStatistic}{limmaGUI}{ChooseEbayesStatistic}
\aliasA{ChooseParameterization}{limmaGUI}{ChooseParameterization}
\aliasA{ChoosePlotSymbolByClicking}{limmaGUI}{ChoosePlotSymbolByClicking}
\aliasA{ChooseSpotType}{limmaGUI}{ChooseSpotType}
\aliasA{ComputeContrasts}{limmaGUI}{ComputeContrasts}
\aliasA{ComputeLinearModel}{limmaGUI}{ComputeLinearModel}
\aliasA{ComputeLinearModelFit}{limmaGUI}{ComputeLinearModelFit}
\aliasA{CopyGraph}{limmaGUI}{CopyGraph}
\aliasA{CreateNewParameterization}{limmaGUI}{CreateNewParameterization}
\aliasA{CreateTreeAndList}{limmaGUI}{CreateTreeAndList}
\aliasA{DeleteContrastsParameterization}{limmaGUI}{DeleteContrastsParameterization}
\aliasA{DeleteCustomMenuItem}{limmaGUI}{DeleteCustomMenuItem}
\aliasA{deleteItemFromList}{limmaGUI}{deleteItemFromList}
\aliasA{DeleteParameterization}{limmaGUI}{DeleteParameterization}
\aliasA{DupCorBoxPlot}{limmaGUI}{DupCorBoxPlot}
\aliasA{ebayesBoxPlots}{limmaGUI}{ebayesBoxPlots}
\aliasA{evalRcode}{limmaGUI}{evalRcode}
\aliasA{ExportAvalues}{limmaGUI}{ExportAvalues}
\aliasA{ExportHTMLreport}{limmaGUI}{ExportHTMLreport}
\aliasA{ExportMvalues}{limmaGUI}{ExportMvalues}
\aliasA{ExportTopTable}{limmaGUI}{ExportTopTable}
\aliasA{fixSeps}{limmaGUI}{fixSeps}
\aliasA{GetBackgroundCorrectionMethod}{limmaGUI}{GetBackgroundCorrectionMethod}
\aliasA{GetBetweenArrayNormalizationMethod}{limmaGUI}{GetBetweenArrayNormalizationMethod}
\aliasA{GetCoef}{limmaGUI}{GetCoef}
\aliasA{GetComponentsToExportInHTMLreport}{limmaGUI}{GetComponentsToExportInHTMLreport}
\aliasA{GetContrastsParameterizationName}{limmaGUI}{GetContrastsParameterizationName}
\aliasA{GetContrastsParameterizationNames}{limmaGUI}{GetContrastsParameterizationNames}
\aliasA{GetCustomMenuItemNum}{limmaGUI}{GetCustomMenuItemNum}
\aliasA{GetDEcutoff}{limmaGUI}{GetDEcutoff}
\aliasA{GetDesignOrContrasts}{limmaGUI}{GetDesignOrContrasts}
\aliasA{GetGeneLabelsOptions}{limmaGUI}{GetGeneLabelsOptions}
\aliasA{GetGenePixFlagWeightings}{limmaGUI}{GetGenePixFlagWeightings}
\aliasA{GetImageAnalysisColumnHeadings}{limmaGUI}{GetImageAnalysisColumnHeadings}
\aliasA{GetImageProcessingFileType}{limmaGUI}{GetImageProcessingFileType}
\aliasA{GetJpegOrPngParams}{limmaGUI}{GetJpegOrPngParams}
\aliasA{GetJpegOrPngX11Params}{limmaGUI}{GetJpegOrPngX11Params}
\aliasA{GetlimmaDataSetName}{limmaGUI}{GetlimmaDataSetName}
\aliasA{GetlmFitMethod}{limmaGUI}{GetlmFitMethod}
\aliasA{GetLowessType}{limmaGUI}{GetLowessType}
\aliasA{GetMenuName}{limmaGUI}{GetMenuName}
\aliasA{GetNEWxlim}{limmaGUI}{GetNEWxlim}
\aliasA{GetNumParametersNoTargets}{limmaGUI}{GetNumParametersNoTargets}
\aliasA{getPackageVersion}{limmaGUI}{getPackageVersion}
\aliasA{GetParameterizationName}{limmaGUI}{GetParameterizationName}
\aliasA{GetParameterNames}{limmaGUI}{GetParameterNames}
\aliasA{GetParametersAndOrContrasts}{limmaGUI}{GetParametersAndOrContrasts}
\aliasA{GetPlotLabels}{limmaGUI}{GetPlotLabels}
\aliasA{GetPlotSize}{limmaGUI}{GetPlotSize}
\aliasA{GetPlotTitle}{limmaGUI}{GetPlotTitle}
\aliasA{GetPValueCutoff}{limmaGUI}{GetPValueCutoff}
\aliasA{GetReducedDuplicateSpacing}{limmaGUI}{GetReducedDuplicateSpacing}
\aliasA{GetRNATypesFrom.ContrastsFromDropDowns.String}{limmaGUI}{GetRNATypesFrom.ContrastsFromDropDowns.String}
\aliasA{GetSlideNum}{limmaGUI}{GetSlideNum}
\aliasA{GetSpotTypesForLinearModel}{limmaGUI}{GetSpotTypesForLinearModel}
\aliasA{GetSpotTypesIncludedNames}{limmaGUI}{GetSpotTypesIncludedNames}
\aliasA{GetWithinArrayNormalizationMethod}{limmaGUI}{GetWithinArrayNormalizationMethod}
\aliasA{GetWtAreaParams}{limmaGUI}{GetWtAreaParams}
\aliasA{GetWtFlagParams}{limmaGUI}{GetWtFlagParams}
\aliasA{HeatDiagramDialog}{limmaGUI}{HeatDiagramDialog}
\aliasA{HeatDiagramPlot}{limmaGUI}{HeatDiagramPlot}
\aliasA{HowManyDups}{limmaGUI}{HowManyDups}
\aliasA{HTMLplotUsingFunction}{limmaGUI}{HTMLplotUsingFunction}
\aliasA{ImageArrayPlot}{limmaGUI}{ImageArrayPlot}
\aliasA{ImageArrayPlotDialog}{limmaGUI}{ImageArrayPlotDialog}
\aliasA{imageplotlimmaGUI}{limmaGUI}{imageplotlimmaGUI}
\aliasA{ImportMA}{limmaGUI}{ImportMA}
\aliasA{ImportMADialog}{limmaGUI}{ImportMADialog}
\aliasA{initGlobals}{limmaGUI}{initGlobals}
\aliasA{InitNewParameterization}{limmaGUI}{InitNewParameterization}
\aliasA{limmaGUIhelp}{limmaGUI}{limmaGUIhelp}
\aliasA{limmaHelp}{limmaGUI}{limmaHelp}
\aliasA{lmFitMethodHelp}{limmaGUI}{lmFitMethodHelp}
\aliasA{LogOddsPlot}{limmaGUI}{LogOddsPlot}
\aliasA{MAPlot}{limmaGUI}{MAPlot}
\aliasA{MAPlotAvg}{limmaGUI}{MAPlotAvg}
\aliasA{MBoxPlot}{limmaGUI}{MBoxPlot}
\aliasA{MMPlot}{limmaGUI}{MMPlot}
\aliasA{NewLimmaFile}{limmaGUI}{NewLimmaFile}
\aliasA{NormalizeNow}{limmaGUI}{NormalizeNow}
\aliasA{nstrstr}{limmaGUI}{nstrstr}
\aliasA{onDestroy}{limmaGUI}{onDestroy}
\aliasA{onExit}{limmaGUI}{onExit}
\aliasA{OpenALimmaFile}{limmaGUI}{OpenALimmaFile}
\aliasA{OpenGALandTargetsandSpotTypesfiles}{limmaGUI}{OpenGALandTargetsandSpotTypesfiles}
\aliasA{OpenGALFile}{limmaGUI}{OpenGALFile}
\aliasA{OpenLimmaFile}{limmaGUI}{OpenLimmaFile}
\aliasA{OpenSpotTypesFile}{limmaGUI}{OpenSpotTypesFile}
\aliasA{OpenTargetsFile}{limmaGUI}{OpenTargetsFile}
\aliasA{plotMAColorCoded}{limmaGUI}{plotMAColorCoded}
\aliasA{PlotOptions}{limmaGUI}{PlotOptions}
\aliasA{PrintTipGroupMAPlot}{limmaGUI}{PrintTipGroupMAPlot}
\aliasA{QQTplot}{limmaGUI}{QQTplot}
\aliasA{read.marrayTools}{limmaGUI}{read.marrayTools}
\aliasA{readGALlimmaGUI}{limmaGUI}{readGALlimmaGUI}
\aliasA{ReadImageProcessingFiles}{limmaGUI}{ReadImageProcessingFiles}
\aliasA{Require}{limmaGUI}{Require}
\aliasA{Resize}{limmaGUI}{Resize}
\aliasA{SaveAsLimmaFile}{limmaGUI}{SaveAsLimmaFile}
\aliasA{SaveGraphAsJpeg}{limmaGUI}{SaveGraphAsJpeg}
\aliasA{SaveGraphAsPDF}{limmaGUI}{SaveGraphAsPDF}
\aliasA{SaveGraphAsPNG}{limmaGUI}{SaveGraphAsPNG}
\aliasA{SaveGraphAsPostscript}{limmaGUI}{SaveGraphAsPostscript}
\aliasA{SaveLimmaFile}{limmaGUI}{SaveLimmaFile}
\aliasA{SelectPlotSymbols}{limmaGUI}{SelectPlotSymbols}
\aliasA{SetLayoutParameters}{limmaGUI}{SetLayoutParameters}
\aliasA{SetupPlotKeyBindings}{limmaGUI}{SetupPlotKeyBindings}
\aliasA{SetupPlotMenus}{limmaGUI}{SetupPlotMenus}
\aliasA{SetWD}{limmaGUI}{SetWD}
\aliasA{showGAL}{limmaGUI}{showGAL}
\aliasA{showTopTable}{limmaGUI}{showTopTable}
\aliasA{SimplifyContrastsExpression}{limmaGUI}{SimplifyContrastsExpression}
\aliasA{strstr}{limmaGUI}{strstr}
\aliasA{tclArrayVar}{limmaGUI}{tclArrayVar}
\aliasA{TclRequire}{limmaGUI}{TclRequire}
\aliasA{Try}{limmaGUI}{Try}
\aliasA{TryReadImgProcFile}{limmaGUI}{TryReadImgProcFile}
\aliasA{UpdateSpotTypesStatus}{limmaGUI}{UpdateSpotTypesStatus}
\aliasA{UpDownOrBoth}{limmaGUI}{UpDownOrBoth}
\aliasA{vennDiagramlimmaGUI}{limmaGUI}{vennDiagramlimmaGUI}
\aliasA{VennDiagramPlot}{limmaGUI}{VennDiagramPlot}
\aliasA{ViewDesignOrContrastsMatrixAsPairs}{limmaGUI}{ViewDesignOrContrastsMatrixAsPairs}
\aliasA{ViewDesignOrContrastsMatrixInTable}{limmaGUI}{ViewDesignOrContrastsMatrixInTable}
\aliasA{ViewExistingContrastsParameterization}{limmaGUI}{ViewExistingContrastsParameterization}
\aliasA{ViewExistingParameterization}{limmaGUI}{ViewExistingParameterization}
\aliasA{ViewRNATargets}{limmaGUI}{ViewRNATargets}
\aliasA{ViewSpotTypes}{limmaGUI}{ViewSpotTypes}
\aliasA{WithinBetweenOrBoth}{limmaGUI}{WithinBetweenOrBoth}
\aliasA{wtflags2}{limmaGUI}{wtflags2}
\keyword{IO}{limmaGUI}
\begin{Description}\relax
Graphical User Interface for the limma microarray package
\end{Description}
\begin{Usage}
\begin{verbatim}
limmaGUI()
GetComponentsToExportInHTMLreport()
HTMLplotUsingFunction()
ExportTopTable()
ExportHTMLreport()
TryReadImgProcFile()
Require()
TclRequire()
getPackageVersion()
initGlobals()
deleteItemFromList()
SetLayoutParameters()
OpenGALFile()
OpenTargetsFile()
OpenSpotTypesFile()
GetImageProcessingFileType()
ReadImageProcessingFiles()
tclArrayVar()
GetDesignOrContrasts()
SimplifyContrastsExpression()
GetRNATypesFrom.ContrastsFromDropDowns.String()
GetParameterNames()
GetReducedDuplicateSpacing()
GetContrastsParameterizationNames()
GetSpotTypesIncludedNames()
HowManyDups()
ViewDesignOrContrastsMatrixInTable()
ViewDesignOrContrastsMatrixAsPairs()
ViewExistingContrastsParameterization()
ViewExistingParameterization()
CreateNewParameterization()
ViewRNATargets()
nstrstr()
strstr()
ViewSpotTypes()
ComputeContrasts()
ComputeLinearModel()
ChooseParameterization()
GetCoef()
showTopTable()
GetSpotTypesForLinearModel()
GetSlideNum()
GetDEcutoff()
UpdateSpotTypesStatus()
ChooseEbayesStatistic()
ChooseSpotType()
GetWtAreaParams()
GetWtFlagParams()
evalRcode()
OpenGALandTargetsandSpotTypesfiles()
GetlimmaDataSetName()
GetParameterizationName()
GetContrastsParameterizationName()
ImportMA()
ImportMADialog()
NewLimmaFile()
SetWD()
onExit()
DeleteParameterization()
ChooseContrastsParameterization()
DeleteContrastsParameterization()
OpenLimmaFile()
OpenALimmaFile(FileName)
SaveLimmaFile()
SaveAsLimmaFile()
AboutLimmaGUI()
addMenuItem()
GetMenuName()
GetNumParametersNoTargets()
AboutCustomMenu()
DeleteCustomMenuItem()
GetCustomMenuItemNum()
GetWithinArrayNormalizationMethod()
GetBetweenArrayNormalizationMethod()
NormalizeNow()
AboutNormalization()
GetGeneLabelsOptions()
MAPlotAvg()
MMPlot()
GetParametersAndOrContrasts()
HeatDiagramDialog()
HeatDiagramPlot()
ImageArrayPlotDialog()
ImageArrayPlot()
LogOddsPlot()
DupCorBoxPlot()
QQTplot()
MBoxPlot()
PrintTipGroupMAPlot()
MAPlot()
ChoosePlotSymbolByClicking()
SelectPlotSymbols()
plotMAColorCoded()
GetNEWxlim()
ebayesBoxPlots()
GetPlotLabels()
GetPlotTitle()
GetPlotSize()
read.marrayTools(MFile,AFile, path, verbose, sep, quote, header, ...)
Resize()
SaveGraphAsJpeg()
SaveGraphAsPNG()
SaveGraphAsPostscript()
SaveGraphAsPDF()
showGAL()
CopyGraph()
SetupPlotKeyBindings()
SetupPlotMenus()
GetJpegOrPngParams()
GetJpegOrPngX11Params()
VennDiagramPlot()
UpDownOrBoth()
GetBackgroundCorrectionMethod()
GetlmFitMethod()
lmFitMethodHelp()
BChelp()
fixSeps(string)
onDestroy()
limmaGUI(BigfontsForlimmaGUIpresentation=FALSE)
GetPValueCutoff(p.value=0.01)
GetImageAnalysisColumnHeadings()
GetLowessType()
PlotOptions()
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{BigfontsForlimmaGUIpresentation}] If set to TRUE, larger fonts are used.  However, some font 
sizes are not controlled by limmaGUI and so must be adjusted in the operating system, e.g.
in the Control Panel in Windows under Display, Appearance.
\item[\code{MFile}] Flat-file of log-ratios output by marrayTools
\item[\code{AFile}] Flat-file of log-intensities output by marrayTools
\item[\code{path}] Path to the directory containing the MFile and AFile
\item[\code{verbose}] Optional diagnostic messages
\item[\code{sep}] Column separator. ("\t" for tab-delimited text)
\item[\code{quote}] See help for read.table
\item[\code{header}] See help for read.table
\item[\code{p.value}] A p-value cutoff.
\item[\code{FileName}] A file name.
\item[\code{string}] A character string.
\item[\code{...}] Any other arguments to read.marrayTools are passed to \code{read.table}
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function launches a Graphical User Interface for the limma package by Gordon Smyth.
The GUI uses Tk widgets (via the R TclTk interface by Peter Dalgaard) in order to provide
a simple interface to the limma functions for linear modelling of microarrays and 
identification of differentially expressed genes.
\end{Details}
\begin{Author}\relax
James Wettenhall
\end{Author}

