limmaGUI: GUI for limma package with two color microarrays

A Graphical User Interface for differential expression analysis of two-color microarray data using the limma package.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("limmaGUI")
AuthorJames Wettenhall [aut], Gordon Smyth [aut], Keith Satterley [ctb], Yifang Hu [ctb]
Bioconductor views BatchEffect Bayesian DataImport DifferentialExpression GUI GeneExpression Microarray MultipleComparison Normalization Preprocessing QualityControl Regression TimeCourse TwoChannel mRNAMicroarray
Date of publicationNone
MaintainerYifang Hu <hu@wehi.edu.au>, Gordon Smyth <smyth@wehi.edu.au>, Keith Satterley <keith@wehi.edu.au>
LicenseGPL (>=2)
Version1.52.0
http://bioinf.wehi.edu.au/limmaGUI/

View on Bioconductor

Functions

AboutLimmaGUI Man page
AboutNormalization Man page
BChelp Man page
ChooseContrastsParameterization Man page
chooseDir Man page
ChooseEbayesStatistic Man page
ChooseParameterization Man page
ChoosePlotSymbolByClicking Man page
ChooseSpotType Man page
ComputeContrasts Man page
ComputeLinearModelFit Man page
CopyGraph Man page
CreateNewParameterization Man page
CreateTreeAndList Man page
DeleteContrastsParameterization Man page
deleteItemFromList Man page
DeleteParameterization Man page
DupCorBoxPlot Man page
ebayesBoxPlots Man page
evalRcode Man page
ExportAvalues Man page
ExportHTMLreport Man page
ExportMvalues Man page
ExportTopTable Man page
fixSeps Man page
GetBackgroundCorrectionMethod Man page
GetBetweenArrayNormalizationMethod Man page
GetCoef Man page
GetComponentsToExportInHTMLreport Man page
GetContrastsParameterizationName Man page
GetContrastsParameterizationNames Man page
GetDEcutoff Man page
GetDesignOrContrasts Man page
GetGeneLabelsOptions Man page
GetGenePixFlagWeightings Man page
GetImageAnalysisColumnHeadings Man page
GetImageProcessingFileType Man page
GetJpegOrPngParams Man page
GetJpegOrPngX11Params Man page
GetlimmaDataSetName Man page
GetlmFitMethod Man page
GetLowessType Man page
GetNEWxlim Man page
GetNormexpOffsetValue Man page
GetNumParametersNoTargets Man page
getPackageVersion Man page
GetParameterizationName Man page
GetParameterNames Man page
GetParametersAndOrContrasts Man page
GetPlotLabels Man page
GetPlotSize Man page
GetPlotTitle Man page
GetPValueCutoff Man page
GetReducedDuplicateSpacing Man page
GetRNATypesFrom.ContrastsFromDropDowns.String Man page
GetSlideNum Man page
GetSpotTypesForLinearModel Man page
GetSpotTypesIncludedNames Man page
GetWithinArrayNormalizationMethod Man page
GetWtAreaParams Man page
HeatDiagramDialog Man page
HeatDiagramPlot Man page
HowManyDups Man page
HTMLplotUsingFunction Man page
ImageArrayPlot Man page
ImageArrayPlotDialog Man page
imageplotlimmaGUI Man page
ImportMA Man page
ImportMADialog Man page
initGlobals Man page
InitNewParameterization Man page
LGchangeLog Man page
limmaGUI Man page
limmaGUIhelp Man page
limmaHelp Man page
lmFitMethodHelp Man page
LogOddsPlot Man page
MAPlot Man page
MAPlotAvg Man page
MBoxPlot Man page
MMPlot Man page
NewLimmaFile Man page
NormalizeNow Man page
nstrstr Man page
onDestroy Man page
onExit Man page
OpenALimmaFile Man page
OpenGALandTargetsandSpotTypesfiles Man page
OpenGALFile Man page
OpenLimmaFile Man page
OpenSpotTypesFile Man page
OpenTargetsFile Man page
plotMAColorCoded Man page
PlotOptions Man page
PrintTipGroupMAPlot Man page
QQTplot Man page
readGALlimmaGUI Man page
ReadImageProcessingFiles Man page
read.marrayTools Man page
Require Man page
Resize Man page
SaveAsLimmaFile Man page
SaveGraphAsJpeg Man page
SaveGraphAsPDF Man page
SaveGraphAsPNG Man page
SaveGraphAsPostscript Man page
SaveLimmaFile Man page
SelectPlotSymbols Man page
SetLayoutParameters Man page
SetupPlotKeyBindings Man page
SetupPlotMenus Man page
SetWD Man page
showChangeLog Man page
showCitations Man page
showGAL Man page
showTopTable Man page
SimplifyContrastsExpression Man page
strstr Man page
tclArrayVar Man page
TclRequire Man page
Try Man page
TryReadImgProcFile Man page
UpdateSpotTypesStatus Man page
UpDownOrBoth Man page
vennDiagramlimmaGUI Man page
VennDiagramPlot Man page
ViewDesignOrContrastsMatrixAsPairs Man page
ViewDesignOrContrastsMatrixInTable Man page
ViewExistingContrastsParameterization Man page
ViewExistingParameterization Man page
ViewRNATargets Man page
ViewSpotTypes Man page
WithinBetweenOrBoth Man page
wtflags2 Man page

Files

DESCRIPTION
NAMESPACE
R
R/GetBC.R R/PlotOptions.R R/htmlReport.R R/imageAnalysisFormat.R R/import.R R/lmFitMethod.R R/main.R R/normalize.R R/plot.R R/showGAL.R R/utility.R R/zzz.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/ApoAI
inst/doc/ApoAI/ApoAILinearModelComputed.jpg
inst/doc/ApoAI/ApoAIScaleBoxPlot.jpg
inst/doc/ApoAI/ApoAITargets.jpg
inst/doc/ApoAI/AvgMAPlotFittedMValues.jpg
inst/doc/ApoAI/ChooseNormalizationMethod.jpg
inst/doc/ApoAI/ChooseParameter.jpg
inst/doc/ApoAI/ChooseParameterOrContrast.jpg
inst/doc/ApoAI/ChooseParameterization.jpg
inst/doc/ApoAI/ComputeContrastsSelected.jpg
inst/doc/ApoAI/ComputeLinearModelFitSelected.jpg
inst/doc/ApoAI/ContrastsComputed.jpg
inst/doc/ApoAI/ContrastsDropDowns.jpg
inst/doc/ApoAI/ContrastsParameterizationName.jpg
inst/doc/ApoAI/CreateNewParameterization.jpg
inst/doc/ApoAI/DEGeneLabelsOptions.jpg
inst/doc/ApoAI/LogOddsPlot.jpg
inst/doc/ApoAI/LogOddsPlotSelected.jpg
inst/doc/ApoAI/MBoxPlotSelected.jpg
inst/doc/ApoAI/MainWindowApoAILimmaFileLoaded.jpg
inst/doc/ApoAI/NormalizeBetweenArraysNo.jpg
inst/doc/ApoAI/NormalizeWithinArrays.jpg
inst/doc/ApoAI/NumDEGeneLabels.jpg
inst/doc/ApoAI/NumberDuplicates.jpg
inst/doc/ApoAI/OpenSelected.jpg
inst/doc/ApoAI/OpeningLimmaFile.jpg
inst/doc/ApoAI/ParameterizationName.jpg
inst/doc/ApoAI/ParametersDropDowns.jpg
inst/doc/ApoAI/PlotBoxPlotBySlide.jpg
inst/doc/ApoAI/SaveAsSelected.jpg
inst/doc/ApoAI/SavingApoAILimmaFile.jpg
inst/doc/ApoAI/SpotsIncludedInLinearModel.jpg
inst/doc/ApoAI/Toptable.jpg
inst/doc/ApoAI/ToptableContrast.jpg
inst/doc/ApoAI/ToptableOptions.jpg
inst/doc/ApoAI/ToptableSelected.jpg
inst/doc/ApoAI/index.html
inst/doc/ApoAI/limmaGUImainWindow.jpg
inst/doc/Bob
inst/doc/Bob/BobLimmaLoaded.jpg
inst/doc/Bob/CalculateDupCor.jpg
inst/doc/Bob/ChooseNormalizationMethod.jpg
inst/doc/Bob/ChooseParameter.jpg
inst/doc/Bob/ChooseParameterization.jpg
inst/doc/Bob/ComputeLinearModelFitSelected.jpg
inst/doc/Bob/CreateNewParameterizationNo.jpg
inst/doc/Bob/DupCorBoxPlot.jpg
inst/doc/Bob/DupCorBoxPlotSelected.jpg
inst/doc/Bob/DupCorMB.jpg
inst/doc/Bob/LinearModelComputed.jpg
inst/doc/Bob/LogOddsPlot.jpg
inst/doc/Bob/LogOddsPlotSelected.jpg
inst/doc/Bob/NormalizeBetweenArraysNo.jpg
inst/doc/Bob/NormalizeWithinArrays.jpg
inst/doc/Bob/NumberDuplicates.jpg
inst/doc/Bob/OpenSelected.jpg
inst/doc/Bob/OpeningBobLimma.jpg
inst/doc/Bob/ParameterDropDowns.jpg
inst/doc/Bob/ParameterizationName.jpg
inst/doc/Bob/RNATargets.jpg
inst/doc/Bob/SaveAsSelected.jpg
inst/doc/Bob/SavingBobLinearModelComputed.jpg
inst/doc/Bob/SpotsIncludedInLinearModel.jpg
inst/doc/Bob/Toptable.jpg
inst/doc/Bob/ToptableSelected.jpg
inst/doc/Bob/ZeroDEgeneLabels.jpg
inst/doc/Bob/index.html
inst/doc/Bob/layout.jpg
inst/doc/CustMenu.html
inst/doc/InputFiles.html
inst/doc/LinModIntro.pdf
inst/doc/LinModIntro.tex
inst/doc/Swirl
inst/doc/Swirl/ChooseNormalizationMethod.jpg
inst/doc/Swirl/ChooseParameter.jpg
inst/doc/Swirl/ChooseParameterizationDialog.jpg
inst/doc/Swirl/ChooseSwirlWorkingDir.jpg
inst/doc/Swirl/ComputeLinearModelFitSelected.jpg
inst/doc/Swirl/CreateNewParameterization.jpg
inst/doc/Swirl/DEGeneLabelsOptions.jpg
inst/doc/Swirl/DataSetNameSwirl.jpg
inst/doc/Swirl/EvalRCodeGALexample.jpg
inst/doc/Swirl/EvaluateRCodeSelected.jpg
inst/doc/Swirl/ExportHTMLReportSelected.jpg
inst/doc/Swirl/FileSaveAsSelected.jpg
inst/doc/Swirl/GALTargetsandSpotTypesFilesSelected.jpg
inst/doc/Swirl/HTMLreportComponentsDialog.jpg
inst/doc/Swirl/ImageArrayPlotEnterExpression.jpg
inst/doc/Swirl/ImageArrayPlotSelected.jpg
inst/doc/Swirl/ImageArrayPlotSlide81.jpg
inst/doc/Swirl/ImageProcessingFileType.jpg
inst/doc/Swirl/LayoutParameters.jpg
inst/doc/Swirl/LogOddsPlot.jpg
inst/doc/Swirl/LogOddsPlotSelected.jpg
inst/doc/Swirl/MAColorCodedScatterPlotSwirlFileClose.jpg
inst/doc/Swirl/MAColorCodedScatterPlotSwirlSlide93.jpg
inst/doc/Swirl/MAPlotFittedMValues.jpg
inst/doc/Swirl/MAPlotFittedMValuesSelected.jpg
inst/doc/Swirl/MAScatterSlide81.jpg
inst/doc/Swirl/MBoxPlotByPrintTipGroup.jpg
inst/doc/Swirl/MBoxPlotSelectedFromMenu.jpg
inst/doc/Swirl/NormalizeBetweenArraysNo.jpg
inst/doc/Swirl/NormalizeBetweenArraysYes.jpg
inst/doc/Swirl/NormalizeWithinArrays.jpg
inst/doc/Swirl/NumDuplicatesDialog.jpg
inst/doc/Swirl/OpenGALandTargetsandSpotTypesFiles.jpg
inst/doc/Swirl/OpenTargetsFileDialog.jpg
inst/doc/Swirl/OpeningFishGAL.jpg
inst/doc/Swirl/OpeningWeaverLimmaFile.jpg
inst/doc/Swirl/PNGImageParametersForHTML.jpg
inst/doc/Swirl/PlotBoxPlotBySlide.jpg
inst/doc/Swirl/PlotByPrintTipGroup.jpg
inst/doc/Swirl/PlotLabelsDialog.jpg
inst/doc/Swirl/PlotPointSymbolsAndColors.jpg
inst/doc/Swirl/PlotTitleForImageArrayPlot.jpg
inst/doc/Swirl/PrintTipGroupMAPlotSelectedFromMenu.jpg
inst/doc/Swirl/PrintTipGroupMAScatterPlotsSlide93.jpg
inst/doc/Swirl/QQTplot.jpg
inst/doc/Swirl/QQTplotSelected.jpg
inst/doc/Swirl/SaveAsSelected.jpg
inst/doc/Swirl/SaveLimmaFileDialog.jpg
inst/doc/Swirl/SavingSwirlHTML.jpg
inst/doc/Swirl/SavingSwirlLimmaFile.jpg
inst/doc/Swirl/ScaleBoxPlot.jpg
inst/doc/Swirl/SelectingParameterForSwirlLinearModel.jpg
inst/doc/Swirl/ShowColorCodedSpotTypesNo.jpg
inst/doc/Swirl/ShowTextResults.jpg
inst/doc/Swirl/Slide81Selected.jpg
inst/doc/Swirl/Slide93Chosen.jpg
inst/doc/Swirl/SpotQualityWeighting.jpg
inst/doc/Swirl/SpotTypesTable.jpg
inst/doc/Swirl/SpotsIncludedInLinearModel.jpg
inst/doc/Swirl/SwirlChooseParameterization.jpg
inst/doc/Swirl/SwirlColorCodedMAPlotSelectedFromPlotMenu.jpg
inst/doc/Swirl/SwirlDesignMatrix.jpg
inst/doc/Swirl/SwirlGAL.jpg
inst/doc/Swirl/SwirlGetParameter.jpg
inst/doc/Swirl/SwirlLayout.jpg
inst/doc/Swirl/SwirlLimmaFileNameInTitleBar.jpg
inst/doc/Swirl/SwirlLinearModelComputed.jpg
inst/doc/Swirl/SwirlParameterizationAsPairs.jpg
inst/doc/Swirl/SwirlParameterizationName.jpg
inst/doc/Swirl/SwirlQQTplot.jpg
inst/doc/Swirl/SwirlRNATargets.jpg
inst/doc/Swirl/SwirlSpotTypes.jpg
inst/doc/Swirl/SwirlTargets.jpg
inst/doc/Swirl/SwirlTopTable.jpg
inst/doc/Swirl/ToptableOptions.jpg
inst/doc/Swirl/ToptableSelected.jpg
inst/doc/Swirl/UseBackgroundCorrection.jpg
inst/doc/Swirl/ViewExistingParameterizationSelected.jpg
inst/doc/Swirl/galEvalRCodeResults.jpg
inst/doc/Swirl/index.html
inst/doc/Swirl/limmaGUINewFileSelected.jpg
inst/doc/Swirl/limmaGUImainWindow.jpg
inst/doc/Swirl/limmaGUImainWindowSwirlArraysLoaded.jpg
inst/doc/Swirl/mainWindowAfterLinModFit.jpg
inst/doc/Weaver
inst/doc/Weaver/ChooseParameterIA.jpg
inst/doc/Weaver/ChooseParameterizationIA.jpg
inst/doc/Weaver/ChooseParameterizationMt.jpg
inst/doc/Weaver/CreateNewParameterizationNo.jpg
inst/doc/Weaver/CreateNewParameterizationSelected.jpg
inst/doc/Weaver/DesignIALoaded.jpg
inst/doc/Weaver/DesignMatrixDialog.jpg
inst/doc/Weaver/DesignMatrixMt.jpg
inst/doc/Weaver/DropDownsAdvancedSelected.jpg
inst/doc/Weaver/EvaluateSelected.jpg
inst/doc/Weaver/HeatDiagram.jpg
inst/doc/Weaver/IAParameterizationName.jpg
inst/doc/Weaver/IAcreated.jpg
inst/doc/Weaver/IAtoptable.jpg
inst/doc/Weaver/MMPlotCutOffValueDialog.jpg
inst/doc/Weaver/MMPlotSelected.jpg
inst/doc/Weaver/MMplotMutant11Mutant21.jpg
inst/doc/Weaver/MtLinearModelComputed.jpg
inst/doc/Weaver/Mutant11Selected.jpg
inst/doc/Weaver/Mutant21Selected.jpg
inst/doc/Weaver/NormalizeBetweenArraysNo.jpg
inst/doc/Weaver/NormalizeWithinArrays.jpg
inst/doc/Weaver/NumDuplicatesDialog.jpg
inst/doc/Weaver/OpenSelected.jpg
inst/doc/Weaver/OpeningDesignIA.jpg
inst/doc/Weaver/OpeningWeaverLimmaFile.jpg
inst/doc/Weaver/ParameterizationNameMt.jpg
inst/doc/Weaver/PlotScaling.jpg
inst/doc/Weaver/RcodeForHeatDiagram.jpg
inst/doc/Weaver/SavingWeaverIALimma.jpg
inst/doc/Weaver/ShowGraphicalResultsOnly.jpg
inst/doc/Weaver/SpotTypesForLinearModel.jpg
inst/doc/Weaver/SpotsIncludedInLinearModel.jpg
inst/doc/Weaver/ToptableSelectedIA.jpg
inst/doc/Weaver/WeaverIASaveAs.jpg
inst/doc/Weaver/WeaverScaleBoxPlot.jpg
inst/doc/Weaver/WeaverTargets.jpg
inst/doc/Weaver/index.html
inst/doc/about.html
inst/doc/about_files
inst/doc/about_files/BioinfBanner.jpg
inst/doc/about_files/Mutant11vsMutant21ScatterPlot.jpg
inst/doc/about_files/SwirlToptable.jpg
inst/doc/about_files/WeaverMtMMPlotSelected.jpg
inst/doc/about_files/wehilogo.gif
inst/doc/changelog.txt
inst/doc/extract.Rnw
inst/doc/extract.pdf
inst/doc/import
inst/doc/import.html
inst/doc/import/DataSetName.png
inst/doc/import/ImportFilesSelected.png
inst/doc/import/ImportMADialog.png
inst/doc/import/OpeningMFile.png
inst/doc/import/WhetherNormalized.png
inst/doc/import/chooseDir.png
inst/doc/import/importSelected.png
inst/doc/index.html
inst/doc/input
inst/doc/input/ApoAISpotTypesInExcel.png
inst/doc/input/ApoAITargetsInExcel.png
inst/doc/input/ImaGeneTargetsFile.png
inst/doc/input/ScorecardSpotTypesInExcel.png
inst/doc/input/ScorecardsTargetsInExcel.png
inst/doc/input/SwirlSampleInExcel.png
inst/doc/lgDevel.html
inst/doc/limmaGUI.R
inst/doc/limmaGUI.Rnw
inst/doc/limmaGUI.pdf
inst/doc/style.css
inst/doc/windowsFocus.html
inst/etc
inst/etc/hist.R
inst/etc/limmaGUI-menus.txt
inst/etc/recent-files.txt
man
man/LGchangelog.Rd man/limmaGUI.Rd
vignettes
vignettes/extract.Rnw
vignettes/extract.Rnw.txt
vignettes/limmaGUI.Rnw
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