\HeaderA{affylmGUI}{Graphical User Interface for the limma microarray package}{affylmGUI}
\aliasA{AboutaffylmGUI}{affylmGUI}{AboutaffylmGUI}
\aliasA{affyHelp}{affylmGUI}{affyHelp}
\aliasA{affylmGUIhelp}{affylmGUI}{affylmGUIhelp}
\aliasA{affyPlotMA}{affylmGUI}{affyPlotMA}
\aliasA{affyPlotMAcontrast}{affylmGUI}{affyPlotMAcontrast}
\aliasA{ALGlimmaUsersGuide}{affylmGUI}{ALGlimmaUsersGuide}
\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{deleteItemFromList}{affylmGUI}{deleteItemFromList}
\aliasA{DensityPlot}{affylmGUI}{DensityPlot}
\aliasA{DensityPlotAll}{affylmGUI}{DensityPlotAll}
\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{GetDEcutoff}{affylmGUI}{GetDEcutoff}
\aliasA{GetGeneLabelsOptions}{affylmGUI}{GetGeneLabelsOptions}
\aliasA{GetJpegOrPngParams}{affylmGUI}{GetJpegOrPngParams}
\aliasA{GetJpegOrPngX11Params}{affylmGUI}{GetJpegOrPngX11Params}
\aliasA{GetlimmaDataSetName}{affylmGUI}{GetlimmaDataSetName}
\aliasA{GetLogPLMDataChoice}{affylmGUI}{GetLogPLMDataChoice}
\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{GetResidualTypeChoice}{affylmGUI}{GetResidualTypeChoice}
\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{ImageQualityResidualPlot}{affylmGUI}{ImageQualityResidualPlot}
\aliasA{ImageQualityWeightPlot}{affylmGUI}{ImageQualityWeightPlot}
\aliasA{initGlobals}{affylmGUI}{initGlobals}
\aliasA{IntensityHistogram}{affylmGUI}{IntensityHistogram}
\aliasA{IntensityHistogramAll}{affylmGUI}{IntensityHistogramAll}
\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{NUSEPlotAll}{affylmGUI}{NUSEPlotAll}
\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{PlotOptions}{affylmGUI}{PlotOptions}
\aliasA{QQTplot}{affylmGUI}{QQTplot}
\aliasA{RawIntensityBoxPlot}{affylmGUI}{RawIntensityBoxPlot}
\aliasA{Require}{affylmGUI}{Require}
\aliasA{Resize}{affylmGUI}{Resize}
\aliasA{RLEPlotAll}{affylmGUI}{RLEPlotAll}
\aliasA{RNADegradationPlotAll}{affylmGUI}{RNADegradationPlotAll}
\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{showChangeLog}{affylmGUI}{showChangeLog}
\aliasA{showCitations}{affylmGUI}{showCitations}
\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{vennDiagramaffylmGUI}{affylmGUI}{vennDiagramaffylmGUI}
\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()
affyHelp()
affylmGUI(BigfontsForaffylmGUIpresentation=FALSE)
affylmGUIhelp()
affyPlotMA()
affyPlotMAcontrast()
ALGlimmaUsersGuide(view=TRUE)
ChooseCDF()
ChooseContrastParameterization()
chooseDir()
ChooseEbayesStatistic()
ComputeContrasts()
ComputeLinearModelFit()
CopyGraph(img)
DeleteContrastParameterization()
deleteItemFromList(list1,itemName=NULL,index=NULL)
DensityPlot()
DensityPlotAll()
evalRcode()
ExportHTMLreport()
ExportNormalizedExpressionValues()
ExportTopTable()
fixSeps(string)
generalPlotFunction(code="",WindowTitle="")
GetComponentsToExportInHTMLreport(contrastParameterizationIndex=NULL)
GetContrast(contrastParameterizationIndex)
GetContrastNamesForHeatDiagram(numContrasts=2,ContrastNames=c("Contrast 1","Contrast 2"))
GetContrastParameterizationName()
GetContrasts(NumContrasts=0)
GetDEcutoff()
GetGeneLabelsOptions()
GetJpegOrPngParams(graphFileType)
GetJpegOrPngX11Params(graphFileType)
GetlimmaDataSetName()
GetLogPLMDataChoice()
GetMultipleContrasts(contrastParameterizationIndex)
GetNormalizationMethod()
getPackageVersion(pkgName)
GetParameterizationName()
GetPlotLabels(plottitle="",xlabel="",ylabel="")
GetPlotSize()
GetPlotTitle(plottitle="")
GetPValueCutoff(p.value=0.01)
GetResidualTypeChoice()
GetRNATypesFrom.ContrastsFromDropDowns.String(string)
GetSetNames(numSets=2,set1="",set2="",set3="")
GetSlideNum(all=FALSE)
GetSlideNums()
GetWhichProbes(includeBoth=FALSE)
GetWtAreaParams()
GetWtFlagParams()
HeatDiagramDialog(parameterName)
HeatDiagramPlot()
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()
ImageQualityResidualPlot()
ImageQualityWeightPlot()
initGlobals()
IntensityHistogram()
IntensityHistogramAll()
limmaHelp()
LogOddsPlot()
NewLimmaFile()
NormalizedIntensityBoxPlot()
NormalizeNow()
nstrstr(haystack,needle)
NUSEPlotAll()
onDestroy()
onExit()
OpenALimmaFile(FileName)
OpenCDFandTargetsfiles()
OpenCDFFile()
OpenLimmaFile(FileName)
OpenTargetsFile()
PlotOptions()
QQTplot()
RawIntensityBoxPlot()
Require(pkg)
Resize(img,plotFunction)
RLEPlotAll()
RNADegradationPlotAll()
SaveAsLimmaFile()
SaveGraphAsJpeg(initialfile, plotFunction)
SaveGraphAsPDF(initialfile, plotFunction)
SaveGraphAsPNG(initialfile, plotFunction)
SaveGraphAsPostscript(initialfile, plotFunction)
SaveLimmaFile()
SetupPlotKeyBindings(tt,img)
SetupPlotMenus(tt,initialfile,plotFunction,img)
SetWD()
showChangeLog(n = 20)
showCitations()
showTopTable(...,export=FALSE)
SimplifyContrastsExpression(string)
strstr(haystack, needle)
tclArrayVar()
TclRequire(tclPkg)
topTable2(fit, coef = 1, number = 10, genelist = NULL,adjust.method = "holm", sort.by = "B")
toptable2(fit, coef = 1, number = 10, genelist = NULL, A = NULL,eb = NULL, adjust.method = "holm", sort.by = "B", ...)
Try(expr)
TryReadImgProcFile(expr)
UpDownOrBoth()
vennDiagramaffylmGUI(object, include = "both", names, cex = 1.5, mar = rep(1, 4), ...)
VennDiagramPlot()
ViewContrastsMatrixAsPairs(contrastsMatrix, contrastsMatrixList,contrastParameterizationIndex = NULL)
ViewContrastsMatrixInTable(contrastsMatrixList, contrastParameterizationIndex = NULL)
ViewExistingContrastParameterization()
ViewRNATargets()
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{BigfontsForaffylmGUIpresentation}] affylmGUI:arg1: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{...}] HTMLplotUsingFunction:arg14:and:showTopTable:arg1:and:toptable2:arg9:and:vennDiagramaffylmGUI:arg6
\item[\code{Align}] HTMLplotUsingFunction:arg8
\item[\code{all}] GetSlideNum:arg1
\item[\code{BG}] HTMLplotUsingFunction:arg12
\item[\code{Caption}] HTMLplotUsingFunction:arg1
\item[\code{code}] generalPlotFunction: arg1: a code
\item[\code{ContrastNames}] GetContrastNamesForHeatDiagram:arg2
\item[\code{contrastParameterizationIndex}] GetComponentsToExportInHTMLreport:arg1:and:contrastParameterizationIndex:arg1:and:GetContrast:arg1:and:HTMLplotUsingFunction:arg3:and:ViewContrastsMatrixInTable:arg2
\item[\code{export}] showTopTable:arg2
\item[\code{expr}] Try:arg1:and:TryReadImgProcFile:arg1
\item[\code{FileName}] OpenALimmaFile:arg1:and:OpenLimmaFile:arg1
\item[\code{File}] HTMLplotUsingFunction:arg2
\item[\code{GraphAbsoluteDirectory}] HTMLplotUsingFunction:arg4
\item[\code{GraphBorder}] HTMLplotUsingFunction:arg7
\item[\code{GraphFileName}] HTMLplotUsingFunction:arg5
\item[\code{graphFileType}] GetJpegOrPngParams:arg1:and:GetJpegOrPngX11Params:arg1
\item[\code{GraphRelativeDirectory}] HTMLplotUsingFunction:arg3
\item[\code{GraphSaveAs}] HTMLplotUsingFunction:arg6
\item[\code{haystack}] nstrstr:arg1:and:strstr:arg1
\item[\code{Height}] HTMLplotUsingFunction:arg11
\item[\code{img}] Resize:arg1:and:SetupPlotMenus:arg4:and:CopyGraph:arg1:and:SetupPlotKeyBindings:arg2
\item[\code{includeBoth}] GetWhichProbes:arg1
\item[\code{index}] deleteItemFromList:arg3:an index
\item[\code{initialfile}] SetupPlotMenus:arg2:and:SaveGraphAsJpeg:arg1:and:SaveGraphAsPDF:arg1:and:SaveGraphAsPNG:arg1:and:SaveGraphAsPostscript:arg1
\item[\code{itemName}] deleteItemFromList:arg2:an item name
\item[\code{list1}] deleteItemFromList:arg1:a list
\item[\code{needle}] nstrstr:arg2:and:strstr:arg2
\item[\code{NumContrasts}] GetContrasts:arg1
\item[\code{numContrasts}] GetContrastNamesForHeatDiagram:arg1
\item[\code{numSets}] GetSetNames:arg1
\item[\code{p.value}] GetPValueCutoff:arg1:A p-value cutoff.
\item[\code{parameterName}] HeatDiagramDialog:arg1
\item[\code{pkgName}] getPackageVersion:arg1
\item[\code{pkg}] Require:arg1
\item[\code{plotFunction}] Resize:arg2:and:HTMLplotUsingFunction:arg9:and:SetupPlotMenus:arg3:and:SaveGraphAsJpeg:arg2:and:SaveGraphAsPDF:arg2:and:SaveGraphAsPNG:arg2:and:SaveGraphAsPostscript:arg2
\item[\code{plottitle}] GetPlotLabels:arg1:and:GetPlotTitle:arg1
\item[\code{res}] HTMLplotUsingFunction:arg13
\item[\code{set1}] GetSetNames:arg2
\item[\code{set2}] GetSetNames:arg3
\item[\code{set3}] GetSetNames:arg4
\item[\code{string}] fixSeps:arg1:A character string:and:GetRNATypesFrom.ContrastsFromDropDowns.String:arg1:and:SimplifyContrastsExpression:arg1
\item[\code{tclPkg}] TclRequire:arg1
\item[\code{tt}] SetupPlotMenus:arg1:and:SetupPlotKeyBindings:arg1
\item[\code{view}] ALGlimmaUsersGuide:arg1:A boolean determinig if the users'd guide will be viewed
\item[\code{Width}] HTMLplotUsingFunction:arg10
\item[\code{WindowTitle}] generalPlotFunction: arg2: a title
\item[\code{xlabel}] GetPlotLabels:arg2
\item[\code{ylabel}] GetPlotLabels:arg3
\item[\code{fit}] topTable2:arg1:and:toptable2:arg1
\item[\code{coef}] topTable2:arg2:and:toptable2:arg2
\item[\code{number}] topTable2:arg3:and:toptable2:arg3
\item[\code{genelist}] topTable2:arg4:and:toptable2:arg4
\item[\code{A}] toptable2:arg5
\item[\code{eb}] toptable2:arg6
\item[\code{adjust.method}] topTable2:arg5:and:toptable2:arg7
\item[\code{sort.by}] topTable2:arg6:and:toptable2:arg8
\item[\code{object}] vennDiagramaffylmGUI:arg1
\item[\code{include}] vennDiagramaffylmGUI:arg2
\item[\code{names}] vennDiagramaffylmGUI:arg3
\item[\code{cex}] vennDiagramaffylmGUI:arg4
\item[\code{mar}] vennDiagramaffylmGUI:arg5
\item[\code{contrastsMatrix}] ViewContrastsMatrixAsPairs:arg1
\item[\code{contrastsMatrixList}] ViewContrastsMatrixAsPairs:arg2:and:ViewContrastsMatrixInTable:arg1
\item[\code{n}] showChangeLog:arg1
\item[\code{PointSize}] HTMLplotUsingFunction:arg12
\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}

