# GUI for affy analysis using limma package

## Documentation for package ‘affylmGUI’ version 1.26.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

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

## -- A --

AboutaffylmGUI | Graphical User Interface for the limma microarray package
affyHelp | Graphical User Interface for the limma microarray package
affylmGUI | Graphical User Interface for the limma microarray package
affylmGUIhelp | Graphical User Interface for the limma microarray package
affyPlotMA | Graphical User Interface for the limma microarray package
affyPlotMAcontrast | Graphical User Interface for the limma microarray package
ALGchangeLog | affylmGUI Change Log
ALGlimmaUsersGuide | Graphical User Interface for the limma microarray package

## -- C --

ChooseCDF | Graphical User Interface for the limma microarray package
ChooseContrastParameterization | 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
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

## -- D --

DeleteContrastParameterization | Graphical User Interface for the limma microarray package
deleteItemFromList | Graphical User Interface for the limma microarray package
DensityPlot | Graphical User Interface for the limma microarray package
DensityPlotAll | Graphical User Interface for the limma microarray package

## -- E --

evalRcode | Graphical User Interface for the limma microarray package
ExportHTMLreport | Graphical User Interface for the limma microarray package
ExportNormalizedExpressionValues | 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 --

generalPlotFunction | Graphical User Interface for the limma microarray package
GetComponentsToExportInHTMLreport | Graphical User Interface for the limma microarray package
GetContrast | Graphical User Interface for the limma microarray package
GetContrastNamesForHeatDiagram | Graphical User Interface for the limma microarray package
GetContrastParameterizationName | Graphical User Interface for the limma microarray package
GetContrasts | Graphical User Interface for the limma microarray package
GetDEcutoff | Graphical User Interface for the limma microarray package
GetGeneLabelsOptions | 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
GetLogPLMDataChoice | Graphical User Interface for the limma microarray package
GetMultipleContrasts | Graphical User Interface for the limma microarray package
GetNormalizationMethod | 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
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
GetResidualTypeChoice | Graphical User Interface for the limma microarray package
GetRNATypesFrom.ContrastsFromDropDowns.String | Graphical User Interface for the limma microarray package
GetSetNames | Graphical User Interface for the limma microarray package
GetSlideNum | Graphical User Interface for the limma microarray package
GetSlideNums | Graphical User Interface for the limma microarray package
GetWhichProbes | Graphical User Interface for the limma microarray package
GetWtAreaParams | Graphical User Interface for the limma microarray package
GetWtFlagParams | 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
HTMLplotUsingFunction | Graphical User Interface for the limma microarray package

## -- I --

ImageArrayPlot | Graphical User Interface for the limma microarray package
ImageQualityResidualPlot | Graphical User Interface for the limma microarray package
ImageQualityWeightPlot | Graphical User Interface for the limma microarray package
initGlobals | Graphical User Interface for the limma microarray package
IntensityHistogram | Graphical User Interface for the limma microarray package
IntensityHistogramAll | Graphical User Interface for the limma microarray package

## -- L --

limmaHelp | Graphical User Interface for the limma microarray package
LogOddsPlot | Graphical User Interface for the limma microarray package

## -- N --

NewLimmaFile | Graphical User Interface for the limma microarray package
NormalizedIntensityBoxPlot | 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
NUSEPlotAll | 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
OpenCDFandTargetsfiles | Graphical User Interface for the limma microarray package
OpenCDFFile | Graphical User Interface for the limma microarray package
OpenLimmaFile | Graphical User Interface for the limma microarray package
OpenTargetsFile | Graphical User Interface for the limma microarray package

## -- P --

PlotOptions | Graphical User Interface for the limma microarray package

## -- Q --

QQTplot | Graphical User Interface for the limma microarray package

## -- R --

RawIntensityBoxPlot | 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
RLEPlotAll | Graphical User Interface for the limma microarray package
RNADegradationPlotAll | 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
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
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
topTable2 | Graphical User Interface for the limma microarray package
toptable2 | 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 --

UpDownOrBoth | Graphical User Interface for the limma microarray package

## -- V --

vennDiagramaffylmGUI | Graphical User Interface for the limma microarray package
VennDiagramPlot | Graphical User Interface for the limma microarray package
ViewContrastsMatrixAsPairs | Graphical User Interface for the limma microarray package
ViewContrastsMatrixInTable | Graphical User Interface for the limma microarray package
ViewExistingContrastParameterization | Graphical User Interface for the limma microarray package
ViewRNATargets | Graphical User Interface for the limma microarray package