\HeaderA{limmaGUI}{Graphical User Interface for the limma microarray package}{limmaGUI}
\aliasA{AboutLimmaGUI}{limmaGUI}{AboutLimmaGUI}
\aliasA{AboutNormalization}{limmaGUI}{AboutNormalization}
\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{ComputeLinearModelFit}{limmaGUI}{ComputeLinearModelFit}
\aliasA{CopyGraph}{limmaGUI}{CopyGraph}
\aliasA{CreateNewParameterization}{limmaGUI}{CreateNewParameterization}
\aliasA{CreateTreeAndList}{limmaGUI}{CreateTreeAndList}
\aliasA{DeleteContrastsParameterization}{limmaGUI}{DeleteContrastsParameterization}
\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{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{GetNEWxlim}{limmaGUI}{GetNEWxlim}
\aliasA{GetNormexpOffsetValue}{limmaGUI}{GetNormexpOffsetValue}
\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{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{limmaUsersGuide}{limmaGUI}{limmaUsersGuide}
\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{showChangeLog}{limmaGUI}{showChangeLog}
\aliasA{showCitations}{limmaGUI}{showCitations}
\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}
AboutLimmaGUI()
AboutNormalization()
BChelp()
ChooseContrastsParameterization(parameterizationTreeIndex)
ChooseEbayesStatistic()
ChooseParameterization()
ChoosePlotSymbolByClicking(spotType, cex)
ChooseSpotType(parameterizationTreeIndex)
ComputeContrasts()
CopyGraph(img)
CreateNewParameterization()
DeleteContrastsParameterization()
deleteItemFromList(list1, itemName = NULL, index = NULL)
DeleteParameterization()
DupCorBoxPlot()
ebayesBoxPlots()
evalRcode()
ExportHTMLreport()
ExportTopTable()
fixSeps(string)
GetBackgroundCorrectionMethod()
GetBetweenArrayNormalizationMethod()
GetCoef(parameterizationTreeIndex, whichCoef = "onlyOne")
GetComponentsToExportInHTMLreport(parameterizationIndex = NULL)
GetContrastsParameterizationName()
GetContrastsParameterizationNames(parameterizationTreeIndex)
GetDEcutoff()
GetDesignOrContrasts(Design = FALSE, Contrasts = FALSE, NumContrasts = 0,parameterizationIndex = 0)
GetGeneLabelsOptions()
GetImageAnalysisColumnHeadings()
GetImageProcessingFileType()
GetJpegOrPngParams(graphFileType)
GetJpegOrPngX11Params(graphFileType)
GetlimmaDataSetName()
GetlmFitMethod()
GetLowessType()
GetNEWxlim(xlim)
GetNormexpOffsetValue(CurrentNormexpOffsetValue)
GetNumParametersNoTargets()
getPackageVersion(pkgName)
GetParameterizationName()
GetParameterNames(parameterizationTreeIndex)
GetParametersAndOrContrasts(parameterizationTreeIndex, whatFor = "heat")
GetPlotLabels(plottitle = "", xlabel = "", ylabel = "")
GetPlotSize()
GetPlotTitle(plottitle = "")
GetPValueCutoff(p.value=0.01)
GetReducedDuplicateSpacing(parameterizationTreeIndex)
GetRNATypesFrom.ContrastsFromDropDowns.String(string)
GetSlideNum()
GetSpotTypesForLinearModel()
GetSpotTypesIncludedNames(parameterizationTreeIndex)
GetWithinArrayNormalizationMethod()
GetWtAreaParams()
HeatDiagramDialog(parameterName)
HeatDiagramPlot()
HowManyDups()
HTMLplotUsingFunction(Caption = "", File = .HTML.file,
                 GraphRelativeDirectory = ".", GraphAbsoluteDirectory =
                 NULL, GraphFileName = "", GraphSaveAs = "png",
                 GraphBorder = 1, Align = "center", plotFunction =
                 NULL, Width = 600, Height = 600, PointSize = 12, BG =
                 "white", res = 72, ...)
ImageArrayPlot()
ImageArrayPlotDialog(slidenum)
ImportMA()
ImportMADialog()
initGlobals()
InitNewParameterization()
limmaGUI(BigfontsForlimmaGUIpresentation=FALSE)
limmaHelp()
limmaUsersGuide(view = TRUE)
lmFitMethodHelp()
LogOddsPlot()
MAPlot()
MAPlotAvg()
MBoxPlot()
MMPlot()
NewLimmaFile()
NormalizeNow()
nstrstr(haystack, needle)
onDestroy()
onExit()
OpenALimmaFile(FileName)
OpenGALandTargetsandSpotTypesfiles()
OpenGALFile()
OpenLimmaFile()
OpenSpotTypesFile()
OpenTargetsFile()
plotMAColorCoded()
PlotOptions()
PrintTipGroupMAPlot()
QQTplot()
read.marrayTools(MFile,AFile, path, verbose, sep, quote, header, ...)
ReadImageProcessingFiles()
Require(pkg)
Resize(img, plotFunction)
SaveAsLimmaFile()
SaveGraphAsJpeg(initialfile, plotFunction)
SaveGraphAsPDF(initialfile, plotFunction)
SaveGraphAsPNG(initialfile, plotFunction)
SaveGraphAsPostscript(initialfile, plotFunction)
SaveLimmaFile()
SelectPlotSymbols(SpotTypes)
SetLayoutParameters()
SetupPlotKeyBindings(tt, img)
SetupPlotMenus(tt, initialfile, plotFunction, img)
SetWD()
showChangeLog()
showCitations()
showGAL()
showTopTable(..., export = FALSE)
SimplifyContrastsExpression(string)
strstr(haystack, needle)
tclArrayVar()
TclRequire(tclPkg)
TryReadImgProcFile(expr)
UpdateSpotTypesStatus()
UpDownOrBoth()
VennDiagramPlot()
ViewDesignOrContrastsMatrixAsPairs(DesignOrContrasts, designOrContrastsList,
                 parameterizationIndex, contrastsParameterizationIndex
                 = NULL)
ViewDesignOrContrastsMatrixInTable(DesignOrContrasts, designOrContrastsList,
                 parameterizationIndex, contrastsParameterizationIndex
                 = NULL)
ViewExistingContrastsParameterization()
ViewExistingParameterization()
ViewRNATargets()
ViewSpotTypes()
\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{...}] 
\item[\code{AFile}] 
\item[\code{Align}] 
\item[\code{BG}] 
\item[\code{Caption}] 
\item[\code{cex}] 
\item[\code{contrastsParameterizationIndex}] ViewDesignOrContrastsMatrixInTable:arg4,ViewDesignOrContrastsMatrixAsPairs:arg4
\item[\code{Contrasts}] 
\item[\code{CurrentNormexpOffsetValue}] 
\item[\code{designOrContrastsList}] 
\item[\code{DesignOrContrasts}] 
\item[\code{Design}] 
\item[\code{export}] 
\item[\code{expr}] 
\item[\code{FileName}] 
\item[\code{File}] 
\item[\code{GraphAbsoluteDirectory}] 
\item[\code{GraphBorder}] 
\item[\code{GraphFileName}] 
\item[\code{graphFileType}] 
\item[\code{GraphRelativeDirectory}] 
\item[\code{GraphSaveAs}] 
\item[\code{haystack}] 
\item[\code{header}] 
\item[\code{Height}] 
\item[\code{img}] 
\item[\code{index}] 
\item[\code{initialfile}] 
\item[\code{itemName}] 
\item[\code{list1}] 
\item[\code{MFile}] 
\item[\code{needle}] 
\item[\code{NumContrasts}] 
\item[\code{p.value}] 
\item[\code{parameterizationIndex}] 
\item[\code{parameterizationTreeIndex}] 
\item[\code{parameterName}] 
\item[\code{path}] 
\item[\code{pkgName}] 
\item[\code{pkg}] 
\item[\code{plotFunction}] 
\item[\code{plottitle}] 
\item[\code{PointSize}] 
\item[\code{quote}] 
\item[\code{res}] 
\item[\code{sep}] 
\item[\code{slidenum}] 
\item[\code{spotType}] 
\item[\code{SpotTypes}] 
\item[\code{string}] 
\item[\code{tclPkg}] 
\item[\code{tt}] 
\item[\code{verbose}] 
\item[\code{view}] 
\item[\code{whatFor}] 
\item[\code{whichCoef}] 
\item[\code{Width}] 
\item[\code{xlabel}] 
\item[\code{xlim}] 
\item[\code{ylabel}] 
\end{ldescription}
                        {GetPlotLabels:arg3}
\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}

