# GUI for limma Package with Affymetrix Microarrays

## Documentation for package ‘affylmGUI’ version 1.80.0

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

## Help Pages

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

affylmGUI-package | The affylmGUI Package: Graphical User Interface for limma analysis of Affymetrix microarrays

## -- A --

AboutaffylmGUI | Internal Functions
affyHelp | Internal Functions
affylmGUI | Graphical User Interface for the limma microarray package
affylmGUIhelp | Internal Functions
affyPlotMA | Internal Functions
affyPlotMAcontrast | Internal Functions

## -- C --

ChooseCDF | Internal Functions
ChooseContrastParameterization | Internal Functions
chooseDir | Internal Functions
ChooseEbayesStatistic | Internal Functions
ComputeContrasts | Internal Functions
ComputeLinearModelFit | Internal Functions
CopyGraph | Internal Functions

## -- D --

DeleteContrastParameterization | Internal Functions
DensityPlot | Internal Functions
DensityPlotAll | Internal Functions

## -- E --

evalRcode | Internal Functions
ExportHTMLreport | Internal Functions
ExportNormalizedExpressionValues | Internal Functions
ExportTopTable | Internal Functions

## -- F --

fixSeps | Internal Functions

## -- G --

generalPlotFunction | Internal Functions
GetComponentsToExportInHTMLreport | Internal Functions
GetContrast | Internal Functions
GetContrastNamesForHeatDiagram | Internal Functions
GetContrastParameterizationName | Internal Functions
GetContrasts | Internal Functions
GetDEcutoff | Internal Functions
GetGeneLabelsOptions | Internal Functions
GetJpegOrPngParams | Internal Functions
GetJpegOrPngX11Params | Internal Functions
GetlimmaDataSetName | Internal Functions
GetLogPLMDataChoice | Internal Functions
GetMultipleContrasts | Internal Functions
GetNormalizationMethod | Internal Functions
getPackageVersion | Internal Functions
GetParameterizationName | Internal Functions
GetPlotLabels | Internal Functions
GetPlotSize | Internal Functions
GetPlotTitle | Internal Functions
GetPValueCutoff | Internal Functions
GetResidualTypeChoice | Internal Functions
GetRNATypesFrom.ContrastsFromDropDowns.String | Internal Functions
GetSetNames | Internal Functions
GetSlideNum | Internal Functions
GetSlideNums | Internal Functions
GetWhichProbes | Internal Functions
GetWtAreaParams | Internal Functions
GetWtFlagParams | Internal Functions

## -- H --

HeatDiagramDialog | Internal Functions
HeatDiagramPlot | Internal Functions
HTMLplotUsingFunction | Internal Functions

## -- I --

ImageArrayPlot | Internal Functions
ImageQualityResidualPlot | Internal Functions
ImageQualityWeightPlot | Internal Functions
initGlobals | Internal Functions
IntensityHistogram | Internal Functions
IntensityHistogramAll | Internal Functions
internal | Internal Functions

## -- L --

limmaHelp | Internal Functions
LogOddsPlot | Internal Functions

## -- N --

NewLimmaFile | Internal Functions
NormalizedIntensityBoxPlot | Internal Functions
NormalizeNow | Internal Functions
nstrstr | Internal Functions
NUSEPlotAll | Internal Functions

## -- O --

onDestroy | Internal Functions
onExit | Internal Functions
OpenALimmaFile | Internal Functions
OpenCDFandTargetsfiles | Internal Functions
OpenCDFFile | Internal Functions
OpenLimmaFile | Internal Functions
OpenTargetsFile | Internal Functions

## -- P --

PlotOptions | Internal Functions

## -- Q --

QQTplot | Internal Functions

## -- R --

RawIntensityBoxPlot | Internal Functions
Require | Internal Functions
Resize | Internal Functions
RLEPlotAll | Internal Functions
RNADegradationPlotAll | Internal Functions

## -- S --

SaveAsLimmaFile | Internal Functions
SaveGraphAsJpeg | Internal Functions
SaveGraphAsPDF | Internal Functions
SaveGraphAsPNG | Internal Functions
SaveGraphAsPostscript | Internal Functions
SaveLimmaFile | Internal Functions
SetupPlotKeyBindings | Internal Functions
SetupPlotMenus | Internal Functions
SetWD | Internal Functions
showChangeLog | Internal Functions
showCitations | Internal Functions
showTopTable | Internal Functions
SimplifyContrastsExpression | Internal Functions
strstr | Internal Functions

## -- T --

tclArrayVar | Internal Functions
TclRequire | Internal Functions
Try | Internal Functions
TryReadImgProcFile | Internal Functions

## -- U --

UpDownOrBoth | Internal Functions

## -- V --

vennDiagramaffylmGUI | Internal Functions
VennDiagramPlot | Internal Functions
ViewContrastsMatrixAsPairs | Internal Functions
ViewContrastsMatrixInTable | Internal Functions
ViewExistingContrastParameterization | Internal Functions
ViewRNATargets | Internal Functions