\HeaderA{affylmGUI}{Graphical User Interface for the limma microarray package}{affylmGUI}
\aliasA{AboutaffylmGUI}{affylmGUI}{AboutaffylmGUI}
\aliasA{AboutCustomMenu}{affylmGUI}{AboutCustomMenu}
\aliasA{AboutNormalization}{affylmGUI}{AboutNormalization}
\aliasA{addMenuItem}{affylmGUI}{addMenuItem}
\aliasA{affyHelp}{affylmGUI}{affyHelp}
\aliasA{affylmGUIhelp}{affylmGUI}{affylmGUIhelp}
\aliasA{affyPlotMA}{affylmGUI}{affyPlotMA}
\aliasA{affyPlotMAcontrast}{affylmGUI}{affyPlotMAcontrast}
\aliasA{ChooseCDF}{affylmGUI}{ChooseCDF}
\aliasA{ChooseContrastParameterization}{affylmGUI}{ChooseContrastParameterization}
\aliasA{chooseDir}{affylmGUI}{chooseDir}
\aliasA{ChooseEbayesStatistic}{affylmGUI}{ChooseEbayesStatistic}
\aliasA{ComputeContrasts}{affylmGUI}{ComputeContrasts}
\aliasA{ComputeLinearModelFit}{affylmGUI}{ComputeLinearModelFit}
\aliasA{CopyGraph}{affylmGUI}{CopyGraph}
\aliasA{DeleteContrastParameterization}{affylmGUI}{DeleteContrastParameterization}
\aliasA{DeleteCustomMenuItem}{affylmGUI}{DeleteCustomMenuItem}
\aliasA{deleteItemFromList}{affylmGUI}{deleteItemFromList}
\aliasA{DensityPlot}{affylmGUI}{DensityPlot}
\aliasA{evalRcode}{affylmGUI}{evalRcode}
\aliasA{ExportHTMLreport}{affylmGUI}{ExportHTMLreport}
\aliasA{ExportNormalizedExpressionValues}{affylmGUI}{ExportNormalizedExpressionValues}
\aliasA{ExportTopTable}{affylmGUI}{ExportTopTable}
\aliasA{fixSeps}{affylmGUI}{fixSeps}
\aliasA{generalPlotFunction}{affylmGUI}{generalPlotFunction}
\aliasA{GetComponentsToExportInHTMLreport}{affylmGUI}{GetComponentsToExportInHTMLreport}
\aliasA{GetContrast}{affylmGUI}{GetContrast}
\aliasA{GetContrastNamesForHeatDiagram}{affylmGUI}{GetContrastNamesForHeatDiagram}
\aliasA{GetContrastParameterizationName}{affylmGUI}{GetContrastParameterizationName}
\aliasA{GetContrasts}{affylmGUI}{GetContrasts}
\aliasA{GetCustomMenuItemNum}{affylmGUI}{GetCustomMenuItemNum}
\aliasA{GetDEcutoff}{affylmGUI}{GetDEcutoff}
\aliasA{GetGeneLabelsOptions}{affylmGUI}{GetGeneLabelsOptions}
\aliasA{GetJpegOrPngParams}{affylmGUI}{GetJpegOrPngParams}
\aliasA{GetJpegOrPngX11Params}{affylmGUI}{GetJpegOrPngX11Params}
\aliasA{GetlimmaDataSetName}{affylmGUI}{GetlimmaDataSetName}
\aliasA{GetMenuName}{affylmGUI}{GetMenuName}
\aliasA{GetMultipleContrasts}{affylmGUI}{GetMultipleContrasts}
\aliasA{GetNormalizationMethod}{affylmGUI}{GetNormalizationMethod}
\aliasA{getPackageVersion}{affylmGUI}{getPackageVersion}
\aliasA{GetParameterizationName}{affylmGUI}{GetParameterizationName}
\aliasA{GetPlotLabels}{affylmGUI}{GetPlotLabels}
\aliasA{GetPlotSize}{affylmGUI}{GetPlotSize}
\aliasA{GetPlotTitle}{affylmGUI}{GetPlotTitle}
\aliasA{GetPValueCutoff}{affylmGUI}{GetPValueCutoff}
\aliasA{GetRNATypesFrom.ContrastsFromDropDowns.String}{affylmGUI}{GetRNATypesFrom.ContrastsFromDropDowns.String}
\aliasA{GetSetNames}{affylmGUI}{GetSetNames}
\aliasA{GetSlideNum}{affylmGUI}{GetSlideNum}
\aliasA{GetSlideNums}{affylmGUI}{GetSlideNums}
\aliasA{GetWhichProbes}{affylmGUI}{GetWhichProbes}
\aliasA{GetWtAreaParams}{affylmGUI}{GetWtAreaParams}
\aliasA{GetWtFlagParams}{affylmGUI}{GetWtFlagParams}
\aliasA{HeatDiagramDialog}{affylmGUI}{HeatDiagramDialog}
\aliasA{HeatDiagramPlot}{affylmGUI}{HeatDiagramPlot}
\aliasA{HTMLplotUsingFunction}{affylmGUI}{HTMLplotUsingFunction}
\aliasA{ImageArrayPlot}{affylmGUI}{ImageArrayPlot}
\aliasA{ImageQualityPlot}{affylmGUI}{ImageQualityPlot}
\aliasA{initGlobals}{affylmGUI}{initGlobals}
\aliasA{IntensityHistogram}{affylmGUI}{IntensityHistogram}
\aliasA{limmaHelp}{affylmGUI}{limmaHelp}
\aliasA{LogOddsPlot}{affylmGUI}{LogOddsPlot}
\aliasA{NewLimmaFile}{affylmGUI}{NewLimmaFile}
\aliasA{NormalizedIntensityBoxPlot}{affylmGUI}{NormalizedIntensityBoxPlot}
\aliasA{NormalizeNow}{affylmGUI}{NormalizeNow}
\aliasA{nstrstr}{affylmGUI}{nstrstr}
\aliasA{onDestroy}{affylmGUI}{onDestroy}
\aliasA{onExit}{affylmGUI}{onExit}
\aliasA{OpenALimmaFile}{affylmGUI}{OpenALimmaFile}
\aliasA{OpenCDFandTargetsfiles}{affylmGUI}{OpenCDFandTargetsfiles}
\aliasA{OpenCDFFile}{affylmGUI}{OpenCDFFile}
\aliasA{OpenLimmaFile}{affylmGUI}{OpenLimmaFile}
\aliasA{OpenTargetsFile}{affylmGUI}{OpenTargetsFile}
\aliasA{QQTplot}{affylmGUI}{QQTplot}
\aliasA{RawIntensityBoxPlot}{affylmGUI}{RawIntensityBoxPlot}
\aliasA{Require}{affylmGUI}{Require}
\aliasA{Resize}{affylmGUI}{Resize}
\aliasA{SaveAsLimmaFile}{affylmGUI}{SaveAsLimmaFile}
\aliasA{SaveGraphAsJpeg}{affylmGUI}{SaveGraphAsJpeg}
\aliasA{SaveGraphAsPDF}{affylmGUI}{SaveGraphAsPDF}
\aliasA{SaveGraphAsPNG}{affylmGUI}{SaveGraphAsPNG}
\aliasA{SaveGraphAsPostscript}{affylmGUI}{SaveGraphAsPostscript}
\aliasA{SaveLimmaFile}{affylmGUI}{SaveLimmaFile}
\aliasA{SetupPlotKeyBindings}{affylmGUI}{SetupPlotKeyBindings}
\aliasA{SetupPlotMenus}{affylmGUI}{SetupPlotMenus}
\aliasA{SetWD}{affylmGUI}{SetWD}
\aliasA{showTopTable}{affylmGUI}{showTopTable}
\aliasA{SimplifyContrastsExpression}{affylmGUI}{SimplifyContrastsExpression}
\aliasA{strstr}{affylmGUI}{strstr}
\aliasA{tclArrayVar}{affylmGUI}{tclArrayVar}
\aliasA{TclRequire}{affylmGUI}{TclRequire}
\aliasA{topTable2}{affylmGUI}{topTable2}
\aliasA{toptable2}{affylmGUI}{toptable2}
\aliasA{Try}{affylmGUI}{Try}
\aliasA{TryReadImgProcFile}{affylmGUI}{TryReadImgProcFile}
\aliasA{UpDownOrBoth}{affylmGUI}{UpDownOrBoth}
\aliasA{vennDiagramlimmaGUI}{affylmGUI}{vennDiagramlimmaGUI}
\aliasA{VennDiagramPlot}{affylmGUI}{VennDiagramPlot}
\aliasA{ViewContrastsMatrixAsPairs}{affylmGUI}{ViewContrastsMatrixAsPairs}
\aliasA{ViewContrastsMatrixInTable}{affylmGUI}{ViewContrastsMatrixInTable}
\aliasA{ViewExistingContrastParameterization}{affylmGUI}{ViewExistingContrastParameterization}
\aliasA{ViewRNATargets}{affylmGUI}{ViewRNATargets}
\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()
ExportTopTable()
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()
OpenALimmaFile()
OpenLimmaFile(FileName)
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()
fixSeps(string)
affylmGUI(BigfontsForaffylmGUIpresentation=FALSE)
affyHelp()
affylmGUIhelp()
limmaHelp()
onDestroy()
GetPValueCutoff(p.value=0.01)
\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.
\item[\code{p.value}] A p-value cutoff.
\item[\code{FileName}] A file name.
\item[\code{string}] A character string.
\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}

