# GUI for limma Package With Two Color Microarrays

## Documentation for package ‘limmaGUI’ version 1.85.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G H I L M N O P Q R S T U V W

## -- A --

AboutLimmaGUI | Graphical User Interface for the limma microarray package
AboutNormalization | Graphical User Interface for the limma microarray package

## -- B --

BChelp | Graphical User Interface for the limma microarray package

## -- C --

ChooseContrastsParameterization | Graphical User Interface for the limma microarray package
chooseDir | Graphical User Interface for the limma microarray package
ChooseEbayesStatistic | Graphical User Interface for the limma microarray package
ChooseParameterization | Graphical User Interface for the limma microarray package
ChoosePlotSymbolByClicking | Graphical User Interface for the limma microarray package
ChooseSpotType | Graphical User Interface for the limma microarray package
ComputeContrasts | Graphical User Interface for the limma microarray package
ComputeLinearModelFit | Graphical User Interface for the limma microarray package
CopyGraph | Graphical User Interface for the limma microarray package
CreateNewParameterization | Graphical User Interface for the limma microarray package
CreateTreeAndList | Graphical User Interface for the limma microarray package

## -- D --

DeleteContrastsParameterization | Graphical User Interface for the limma microarray package
deleteItemFromList | Graphical User Interface for the limma microarray package
DeleteParameterization | Graphical User Interface for the limma microarray package
DupCorBoxPlot | Graphical User Interface for the limma microarray package

## -- E --

ebayesBoxPlots | Graphical User Interface for the limma microarray package
evalRcode | Graphical User Interface for the limma microarray package
ExportAvalues | Graphical User Interface for the limma microarray package
ExportHTMLreport | Graphical User Interface for the limma microarray package
ExportMvalues | Graphical User Interface for the limma microarray package
ExportTopTable | Graphical User Interface for the limma microarray package

## -- F --

fixSeps | Graphical User Interface for the limma microarray package

## -- G --

GetBackgroundCorrectionMethod | Graphical User Interface for the limma microarray package
GetBetweenArrayNormalizationMethod | Graphical User Interface for the limma microarray package
GetCoef | Graphical User Interface for the limma microarray package
GetComponentsToExportInHTMLreport | Graphical User Interface for the limma microarray package
GetContrastsParameterizationName | Graphical User Interface for the limma microarray package
GetContrastsParameterizationNames | Graphical User Interface for the limma microarray package
GetDEcutoff | Graphical User Interface for the limma microarray package
GetDesignOrContrasts | Graphical User Interface for the limma microarray package
GetGeneLabelsOptions | Graphical User Interface for the limma microarray package
GetGenePixFlagWeightings | Graphical User Interface for the limma microarray package
GetImageAnalysisColumnHeadings | Graphical User Interface for the limma microarray package
GetImageProcessingFileType | Graphical User Interface for the limma microarray package
GetJpegOrPngParams | Graphical User Interface for the limma microarray package
GetJpegOrPngX11Params | Graphical User Interface for the limma microarray package
GetlimmaDataSetName | Graphical User Interface for the limma microarray package
GetlmFitMethod | Graphical User Interface for the limma microarray package
GetLowessType | Graphical User Interface for the limma microarray package
GetNEWxlim | Graphical User Interface for the limma microarray package
GetNormexpOffsetValue | Graphical User Interface for the limma microarray package
GetNumParametersNoTargets | Graphical User Interface for the limma microarray package
getPackageVersion | Graphical User Interface for the limma microarray package
GetParameterizationName | Graphical User Interface for the limma microarray package
GetParameterNames | Graphical User Interface for the limma microarray package
GetParametersAndOrContrasts | Graphical User Interface for the limma microarray package
GetPlotLabels | Graphical User Interface for the limma microarray package
GetPlotSize | Graphical User Interface for the limma microarray package
GetPlotTitle | Graphical User Interface for the limma microarray package
GetPValueCutoff | Graphical User Interface for the limma microarray package
GetReducedDuplicateSpacing | Graphical User Interface for the limma microarray package
GetRNATypesFrom.ContrastsFromDropDowns.String | Graphical User Interface for the limma microarray package
GetSlideNum | Graphical User Interface for the limma microarray package
GetSpotTypesForLinearModel | Graphical User Interface for the limma microarray package
GetSpotTypesIncludedNames | Graphical User Interface for the limma microarray package
GetWithinArrayNormalizationMethod | Graphical User Interface for the limma microarray package
GetWtAreaParams | Graphical User Interface for the limma microarray package

## -- H --

HeatDiagramDialog | Graphical User Interface for the limma microarray package
HeatDiagramPlot | Graphical User Interface for the limma microarray package
HowManyDups | Graphical User Interface for the limma microarray package
HTMLplotUsingFunction | Graphical User Interface for the limma microarray package

## -- I --

ImageArrayPlot | Graphical User Interface for the limma microarray package
ImageArrayPlotDialog | Graphical User Interface for the limma microarray package
imageplotlimmaGUI | Graphical User Interface for the limma microarray package
ImportMA | Graphical User Interface for the limma microarray package
ImportMADialog | Graphical User Interface for the limma microarray package
initGlobals | Graphical User Interface for the limma microarray package
InitNewParameterization | Graphical User Interface for the limma microarray package

## -- L --

LGchangeLog | LimmaGUI Change Log
limmaGUI | Graphical User Interface for the limma microarray package
limmaGUIhelp | Graphical User Interface for the limma microarray package
limmaHelp | Graphical User Interface for the limma microarray package
lmFitMethodHelp | Graphical User Interface for the limma microarray package
LogOddsPlot | Graphical User Interface for the limma microarray package

## -- M --

MAPlot | Graphical User Interface for the limma microarray package
MAPlotAvg | Graphical User Interface for the limma microarray package
MBoxPlot | Graphical User Interface for the limma microarray package
MMPlot | Graphical User Interface for the limma microarray package

## -- N --

NewLimmaFile | Graphical User Interface for the limma microarray package
NormalizeNow | Graphical User Interface for the limma microarray package
nstrstr | Graphical User Interface for the limma microarray package

## -- O --

onDestroy | Graphical User Interface for the limma microarray package
onExit | Graphical User Interface for the limma microarray package
OpenALimmaFile | Graphical User Interface for the limma microarray package
OpenGALandTargetsandSpotTypesfiles | Graphical User Interface for the limma microarray package
OpenGALFile | Graphical User Interface for the limma microarray package
OpenLimmaFile | Graphical User Interface for the limma microarray package
OpenSpotTypesFile | Graphical User Interface for the limma microarray package
OpenTargetsFile | Graphical User Interface for the limma microarray package

## -- P --

plotMAColorCoded | Graphical User Interface for the limma microarray package
PlotOptions | Graphical User Interface for the limma microarray package
PrintTipGroupMAPlot | Graphical User Interface for the limma microarray package

## -- Q --

QQTplot | Graphical User Interface for the limma microarray package

## -- R --

read.marrayTools | Graphical User Interface for the limma microarray package
readGALlimmaGUI | Graphical User Interface for the limma microarray package
ReadImageProcessingFiles | Graphical User Interface for the limma microarray package
Require | Graphical User Interface for the limma microarray package
Resize | Graphical User Interface for the limma microarray package

## -- S --

SaveAsLimmaFile | Graphical User Interface for the limma microarray package
SaveGraphAsJpeg | Graphical User Interface for the limma microarray package
SaveGraphAsPDF | Graphical User Interface for the limma microarray package
SaveGraphAsPNG | Graphical User Interface for the limma microarray package
SaveGraphAsPostscript | Graphical User Interface for the limma microarray package
SaveLimmaFile | Graphical User Interface for the limma microarray package
SelectPlotSymbols | Graphical User Interface for the limma microarray package
SetLayoutParameters | Graphical User Interface for the limma microarray package
SetupPlotKeyBindings | Graphical User Interface for the limma microarray package
SetupPlotMenus | Graphical User Interface for the limma microarray package
SetWD | Graphical User Interface for the limma microarray package
showChangeLog | Graphical User Interface for the limma microarray package
showCitations | Graphical User Interface for the limma microarray package
showGAL | Graphical User Interface for the limma microarray package
showTopTable | Graphical User Interface for the limma microarray package
SimplifyContrastsExpression | Graphical User Interface for the limma microarray package
strstr | Graphical User Interface for the limma microarray package

## -- T --

tclArrayVar | Graphical User Interface for the limma microarray package
TclRequire | Graphical User Interface for the limma microarray package
Try | Graphical User Interface for the limma microarray package
TryReadImgProcFile | Graphical User Interface for the limma microarray package

## -- U --

UpdateSpotTypesStatus | Graphical User Interface for the limma microarray package
UpDownOrBoth | Graphical User Interface for the limma microarray package

## -- V --

vennDiagramlimmaGUI | Graphical User Interface for the limma microarray package
VennDiagramPlot | Graphical User Interface for the limma microarray package
ViewDesignOrContrastsMatrixAsPairs | Graphical User Interface for the limma microarray package
ViewDesignOrContrastsMatrixInTable | Graphical User Interface for the limma microarray package
ViewExistingContrastsParameterization | Graphical User Interface for the limma microarray package
ViewExistingParameterization | Graphical User Interface for the limma microarray package
ViewRNATargets | Graphical User Interface for the limma microarray package
ViewSpotTypes | Graphical User Interface for the limma microarray package

## -- W --

WithinBetweenOrBoth | Graphical User Interface for the limma microarray package
wtflags2 | Graphical User Interface for the limma microarray package