\Header{affylmGUI}{Graphical User Interface for the limma microarray package}
\alias{AboutaffylmGUI}{affylmGUI}
\alias{AboutCustomMenu}{affylmGUI}
\alias{AboutNormalization}{affylmGUI}
\alias{addMenuItem}{affylmGUI}
\alias{affyHelp}{affylmGUI}
\alias{affylmGUIhelp}{affylmGUI}
\alias{affyPlotMA}{affylmGUI}
\alias{affyPlotMAcontrast}{affylmGUI}
\alias{ChooseCDF}{affylmGUI}
\alias{ChooseContrastParameterization}{affylmGUI}
\alias{chooseDir}{affylmGUI}
\alias{ChooseEbayesStatistic}{affylmGUI}
\alias{ComputeContrasts}{affylmGUI}
\alias{ComputeLinearModelFit}{affylmGUI}
\alias{CopyGraph}{affylmGUI}
\alias{DeleteContrastParameterization}{affylmGUI}
\alias{DeleteCustomMenuItem}{affylmGUI}
\alias{deleteItemFromList}{affylmGUI}
\alias{DensityPlot}{affylmGUI}
\alias{evalRcode}{affylmGUI}
\alias{ExportHTMLreport}{affylmGUI}
\alias{ExportNormalizedExpressionValues}{affylmGUI}
\alias{generalPlotFunction}{affylmGUI}
\alias{GetComponentsToExportInHTMLreport}{affylmGUI}
\alias{GetContrast}{affylmGUI}
\alias{GetContrastNamesForHeatDiagram}{affylmGUI}
\alias{GetContrastParameterizationName}{affylmGUI}
\alias{GetContrasts}{affylmGUI}
\alias{GetCustomMenuItemNum}{affylmGUI}
\alias{GetDEcutoff}{affylmGUI}
\alias{GetGeneLabelsOptions}{affylmGUI}
\alias{GetJpegOrPngParams}{affylmGUI}
\alias{GetJpegOrPngX11Params}{affylmGUI}
\alias{GetlimmaDataSetName}{affylmGUI}
\alias{GetMenuName}{affylmGUI}
\alias{GetMultipleContrasts}{affylmGUI}
\alias{GetNormalizationMethod}{affylmGUI}
\alias{getPackageVersion}{affylmGUI}
\alias{GetParameterizationName}{affylmGUI}
\alias{GetPlotLabels}{affylmGUI}
\alias{GetPlotSize}{affylmGUI}
\alias{GetPlotTitle}{affylmGUI}
\alias{GetRNATypesFrom.ContrastsFromDropDowns.String}{affylmGUI}
\alias{GetSetNames}{affylmGUI}
\alias{GetSlideNum}{affylmGUI}
\alias{GetSlideNums}{affylmGUI}
\alias{GetWhichProbes}{affylmGUI}
\alias{GetWtAreaParams}{affylmGUI}
\alias{GetWtFlagParams}{affylmGUI}
\alias{HeatDiagramDialog}{affylmGUI}
\alias{HeatDiagramPlot}{affylmGUI}
\alias{HTMLplotUsingFunction}{affylmGUI}
\alias{ImageArrayPlot}{affylmGUI}
\alias{ImageQualityPlot}{affylmGUI}
\alias{initGlobals}{affylmGUI}
\alias{IntensityHistogram}{affylmGUI}
\alias{limmaHelp}{affylmGUI}
\alias{LogOddsPlot}{affylmGUI}
\alias{NewLimmaFile}{affylmGUI}
\alias{NormalizedIntensityBoxPlot}{affylmGUI}
\alias{NormalizeNow}{affylmGUI}
\alias{nstrstr}{affylmGUI}
\alias{onDestroy}{affylmGUI}
\alias{onExit}{affylmGUI}
\alias{OpenCDFandTargetsfiles}{affylmGUI}
\alias{OpenCDFFile}{affylmGUI}
\alias{OpenLimmaFile}{affylmGUI}
\alias{OpenTargetsFile}{affylmGUI}
\alias{QQTplot}{affylmGUI}
\alias{RawIntensityBoxPlot}{affylmGUI}
\alias{Require}{affylmGUI}
\alias{Resize}{affylmGUI}
\alias{SaveAsLimmaFile}{affylmGUI}
\alias{SaveGraphAsJpeg}{affylmGUI}
\alias{SaveGraphAsPDF}{affylmGUI}
\alias{SaveGraphAsPNG}{affylmGUI}
\alias{SaveGraphAsPostscript}{affylmGUI}
\alias{SaveLimmaFile}{affylmGUI}
\alias{SetupPlotKeyBindings}{affylmGUI}
\alias{SetupPlotMenus}{affylmGUI}
\alias{SetWD}{affylmGUI}
\alias{showTopTable}{affylmGUI}
\alias{SimplifyContrastsExpression}{affylmGUI}
\alias{strstr}{affylmGUI}
\alias{tclArrayVar}{affylmGUI}
\alias{TclRequire}{affylmGUI}
\alias{topTable2}{affylmGUI}
\alias{toptable2}{affylmGUI}
\alias{Try}{affylmGUI}
\alias{TryReadImgProcFile}{affylmGUI}
\alias{UpDownOrBoth}{affylmGUI}
\alias{vennDiagramlimmaGUI}{affylmGUI}
\alias{VennDiagramPlot}{affylmGUI}
\alias{ViewContrastsMatrixAsPairs}{affylmGUI}
\alias{ViewContrastsMatrixInTable}{affylmGUI}
\alias{ViewExistingContrastParameterization}{affylmGUI}
\alias{ViewRNATargets}{affylmGUI}
\keyword{IO}{affylmGUI}
\begin{Description}\relax
Graphical User Interface for Affy analysis using the limma microarray package
\end{Description}
\begin{Usage}
\begin{verbatim}
AboutaffylmGUI()
AboutCustomMenu()
AboutNormalization()
addMenuItem()
affylmGUI()
affyPlotMA()
affyPlotMAcontrast()
ChooseCDF()
ChooseContrastParameterization()
chooseDir()
ChooseEbayesStatistic()
ComputeContrasts()
ComputeLinearModelFit()
CopyGraph()
DeleteContrastParameterization()
DeleteCustomMenuItem()
deleteItemFromList()
DensityPlot()
evalRcode()
ExportHTMLreport()
ExportNormalizedExpressionValues()
generalPlotFunction()
GetComponentsToExportInHTMLreport()
GetContrast()
GetContrastNamesForHeatDiagram()
GetContrastParameterizationName()
GetContrasts()
GetCustomMenuItemNum()
GetDEcutoff()
GetGeneLabelsOptions()
GetJpegOrPngParams()
GetJpegOrPngX11Params()
GetlimmaDataSetName()
GetMenuName()
GetMultipleContrasts()
GetNormalizationMethod()
getPackageVersion()
GetParameterizationName()
GetPlotLabels()
GetPlotSize()
GetPlotTitle()
GetRNATypesFrom.ContrastsFromDropDowns.String()
GetSetNames()
GetSlideNum()
GetSlideNums()
GetWhichProbes()
GetWtAreaParams()
GetWtFlagParams()
HeatDiagramDialog()
HeatDiagramPlot()
HTMLplotUsingFunction()
ImageArrayPlot()
ImageQualityPlot()
initGlobals()
IntensityHistogram()
LogOddsPlot()
NewLimmaFile()
NormalizedIntensityBoxPlot()
NormalizeNow()
nstrstr()
onExit()
OpenCDFandTargetsfiles()
OpenCDFFile()
OpenLimmaFile()
OpenTargetsFile()
QQTplot()
RawIntensityBoxPlot()
Require()
Resize()
SaveAsLimmaFile()
SaveGraphAsJpeg()
SaveGraphAsPDF()
SaveGraphAsPNG()
SaveGraphAsPostscript()
SaveLimmaFile()
SetupPlotKeyBindings()
SetupPlotMenus()
SetWD()
showTopTable()
SimplifyContrastsExpression()
strstr()
tclArrayVar()
TclRequire()
toptable2()
topTable2()
Try()
TryReadImgProcFile()
UpDownOrBoth()
vennDiagramlimmaGUI()
VennDiagramPlot()
ViewContrastsMatrixAsPairs()
ViewContrastsMatrixInTable()
ViewExistingContrastParameterization()
ViewRNATargets()
affylmGUI(BigfontsForaffylmGUIpresentation=FALSE)
affyHelp()
affylmGUIhelp()
limmaHelp()
onDestroy()
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{BigfontsForaffylmGUIpresentation}] If set to TRUE, larger fonts are used.  However, some font 
sizes are not controlled by affylmGUI and so must be adjusted in the operating system, e.g.
in the Control Panel in Windows under Display, Appearance.
\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}

