affylmGUI: GUI for limma package with Affymetrix microarrays
Version 1.50.0

A Graphical User Interface for analysis of Affymetrix microarray gene expression data using the affy and limma packages.

Browse man pages Browse package API and functions Browse package files

AuthorJames Wettenhall [cre,aut], Ken Simpson [aut], Gordon Smyth [aut], Keith Satterley [ctb], Yifang Hu [ctb]
Bioconductor views BatchEffect Bayesian DataImport DifferentialExpression GUI GeneExpression Microarray MultipleComparison Normalization OneChannel Preprocessing ProprietaryPlatforms QualityControl Regression TimeCourse Transcription mRNAMicroarray
Date of publicationNone
MaintainerYifang Hu <hu@wehi.edu.au>, Gordon Smyth <smyth@wehi.edu.au>, Keith Satterley <keith@wehi.edu.au>
LicenseGPL (>=2)
Version1.50.0
URL http://bioinf.wehi.edu.au/affylmGUI/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("affylmGUI")

Man pages

affylmGUI: Graphical User Interface for the limma microarray package
ALGchangeLog: affylmGUI Change Log

Functions

ALGchangeLog Man page Source code
ALGlimmaUsersGuide Man page Source code
AboutaffylmGUI Man page Source code
ChooseCDF Man page Source code
ChooseContrastParameterization Man page Source code
ChooseEbayesStatistic Man page Source code
ComputeContrasts Man page Source code
ComputeLinearModelFit Man page Source code
CopyGraph Man page Source code
DeleteContrastParameterization Man page Source code
DensityPlot Man page Source code
DensityPlotAll Man page Source code
ExportHTMLreport Man page Source code
ExportNormalizedExpressionValues Man page Source code
ExportTopTable Man page Source code
GetComponentsToExportInHTMLreport Man page Source code
GetContrast Man page Source code
GetContrastNamesForHeatDiagram Man page Source code
GetContrastParameterizationName Man page Source code
GetContrasts Man page Source code
GetDEcutoff Man page Source code
GetGeneLabelsOptions Man page Source code
GetJpegOrPngParams Man page Source code
GetJpegOrPngX11Params Man page Source code
GetLogPLMDataChoice Man page Source code
GetMultipleContrasts Man page Source code
GetNormalizationMethod Man page Source code
GetPValueCutoff Man page Source code
GetParameterizationName Man page Source code
GetPlotLabels Man page Source code
GetPlotSize Man page Source code
GetPlotTitle Man page Source code
GetRNATypesFrom.ContrastsFromDropDowns.String Man page Source code
GetResidualTypeChoice Man page Source code
GetSetNames Man page Source code
GetSlideNum Man page Source code
GetSlideNums Man page Source code
GetWhichProbes Man page Source code
GetWtAreaParams Man page Source code
GetWtFlagParams Man page Source code
GetlimmaDataSetName Man page Source code
HTMLplotUsingFunction Man page
HeatDiagramDialog Man page Source code
HeatDiagramPlot Man page Source code
ImageArrayPlot Man page Source code
ImageQualityResidualPlot Man page Source code
ImageQualityWeightPlot Man page Source code
IntensityHistogram Man page Source code
IntensityHistogramAll Man page Source code
LogOddsPlot Man page Source code
NUSEPlotAll Man page Source code
NewLimmaFile Man page Source code
NormalizeNow Man page Source code
NormalizedIntensityBoxPlot Man page Source code
OpenALimmaFile Man page Source code
OpenCDFFile Man page Source code
OpenCDFandTargetsfiles Man page Source code
OpenLimmaFile Man page Source code
OpenTargetsFile Man page Source code
PlotOptions Man page Source code
QQTplot Man page Source code
RLEPlotAll Man page Source code
RNADegradationPlotAll Man page Source code
RawIntensityBoxPlot Man page Source code
Require Man page Source code
Resize Man page Source code
SaveAsLimmaFile Man page Source code
SaveGraphAsJpeg Man page Source code
SaveGraphAsPDF Man page Source code
SaveGraphAsPNG Man page Source code
SaveGraphAsPostscript Man page Source code
SaveLimmaFile Man page Source code
SetWD Man page Source code
SetupPlotKeyBindings Man page Source code
SetupPlotMenus Man page Source code
SimplifyContrastsExpression Man page Source code
TclRequire Man page Source code
Try Man page Source code
TryReadImgProcFile Man page Source code
UpDownOrBoth Man page Source code
VennDiagramPlot Man page Source code
ViewContrastsMatrixAsPairs Man page Source code
ViewContrastsMatrixInTable Man page Source code
ViewExistingContrastParameterization Man page Source code
ViewRNATargets Man page Source code
affyHelp Man page Source code
affyPlotMA Man page Source code
affyPlotMAcontrast Man page Source code
affylmGUI Man page Source code
affylmGUIhelp Man page Source code
chooseDir Man page Source code
deleteItemFromList Man page Source code
evalRcode Man page Source code
fixSeps Man page Source code
generalPlotFunction Man page Source code
getPackageVersion Man page Source code
initGlobals Man page Source code
limmaHelp Man page Source code
nstrstr Man page Source code
onAttach Source code
onDestroy Man page
onExit Man page Source code
showChangeLog Man page Source code
showCitations Man page Source code
showTopTable Man page Source code
strstr Man page Source code
tclArrayVar Man page Source code
topTable2 Man page Source code
toptable2 Man page Source code
vennDiagramaffylmGUI Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/PlotOptions.R
R/htmlReport.R
R/main.R
R/normalize.R
R/plot.R
R/toptable.R
R/utility.R
R/zzz.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/CustMenu.html
inst/doc/LifeCycle
inst/doc/LifeCycle/ChooseContrast.png
inst/doc/LifeCycle/ChooseContrastsParameterization.png
inst/doc/LifeCycle/ComputeContrastsSelected.png
inst/doc/LifeCycle/ComputeLinearModelFitSelected.png
inst/doc/LifeCycle/ContrastsDefined.png
inst/doc/LifeCycle/ContrastsName.png
inst/doc/LifeCycle/DEgeneLabelOptions.png
inst/doc/LifeCycle/DataSetName.png
inst/doc/LifeCycle/ExportHTMLselected.png
inst/doc/LifeCycle/HTMLcomponents.png
inst/doc/LifeCycle/HTMLfilename.png
inst/doc/LifeCycle/LifeCycle.html
inst/doc/LifeCycle/MAcontrastPlot.png
inst/doc/LifeCycle/MAcontrastPlotLabels.png
inst/doc/LifeCycle/MAplotContrast.png
inst/doc/LifeCycle/MalariaLifeCycle.html
inst/doc/LifeCycle/MalariaLifeCycle_files
inst/doc/LifeCycle/MalariaLifeCycle_files/NormalizedIntensityBoxPlot.png
inst/doc/LifeCycle/MalariaLifeCycle_files/RawIntensityBoxPlot.png
inst/doc/LifeCycle/MalariaLifeCycle_files/contrastMAplot.1.png
inst/doc/LifeCycle/MalariaLifeCycle_files/contrastMAplot.2.png
inst/doc/LifeCycle/MalariaLifeCycle_files/contrastMAplot.3.png
inst/doc/LifeCycle/MalariaLifeCycle_files/contrastMAplot.4.png
inst/doc/LifeCycle/MalariaLifeCycle_files/contrastMAplot.5.png
inst/doc/LifeCycle/MalariaLifeCycle_files/contrastMAplot.6.png
inst/doc/LifeCycle/NewSelected.png
inst/doc/LifeCycle/NormalizeSelected.png
inst/doc/LifeCycle/PNGparams.png
inst/doc/LifeCycle/R2HTML.css
inst/doc/LifeCycle/R2HTMLlogo.gif
inst/doc/LifeCycle/R2HTMLlogo.png
inst/doc/LifeCycle/RMAselected.png
inst/doc/LifeCycle/TargetsFileSelected.png
inst/doc/LifeCycle/ToptableMzvsLS.png
inst/doc/LifeCycle/ToptableOptions.png
inst/doc/LifeCycle/ToptableSelected.png
inst/doc/LifeCycle/chooseDir.png
inst/doc/LifeCycle/mainWin.png
inst/doc/LifeCycle/malariaTargetsInExcel.png
inst/doc/about.html
inst/doc/about_files
inst/doc/about_files/BioinfBanner.jpg
inst/doc/about_files/HeatDiagram.png
inst/doc/about_files/MAplotPres10vsAbs10.png
inst/doc/about_files/MainWinAfterContrastsComputed.png
inst/doc/about_files/Toptable.png
inst/doc/about_files/wehilogo.gif
inst/doc/affylmGUI.R
inst/doc/affylmGUI.Rnw
inst/doc/affylmGUI.pdf
inst/doc/changelog.txt
inst/doc/estrogen
inst/doc/estrogen/AdvancedButtonShowsContrastsMatrix.png
inst/doc/estrogen/ChooseContrast.png
inst/doc/estrogen/ChooseContrast2.png
inst/doc/estrogen/ChooseContrastsParameterization.png
inst/doc/estrogen/ChooseNormalizationMethod.png
inst/doc/estrogen/ChooseProbSetForDensity.png
inst/doc/estrogen/ChooseSlide.png
inst/doc/estrogen/ComputeContrastsSelected.png
inst/doc/estrogen/ContrastNamesForHeatDiagram.png
inst/doc/estrogen/ContrastsParameterizationName.png
inst/doc/estrogen/DEGeneLabelOptions.png
inst/doc/estrogen/DataSetName.png
inst/doc/estrogen/DefiningContrasts.png
inst/doc/estrogen/DensityPlot.png
inst/doc/estrogen/DensityPlotSelected.png
inst/doc/estrogen/ExportNormalizedExpressionValuesSelected.png
inst/doc/estrogen/ExportingExpressionValues.png
inst/doc/estrogen/ExprsInExcel.png
inst/doc/estrogen/FilenameInTitlebar.png
inst/doc/estrogen/HeatDiagram.png
inst/doc/estrogen/HeatDiagramCutoffs.png
inst/doc/estrogen/HeatDiagramSelected.png
inst/doc/estrogen/ImageArrayPlotSelected.png
inst/doc/estrogen/ImagePlotInR.png
inst/doc/estrogen/ImageQualityPlotInR.png
inst/doc/estrogen/ImageQualityPlotSelected.png
inst/doc/estrogen/LinearModelFitSelected.png
inst/doc/estrogen/LogOddsPlot.png
inst/doc/estrogen/LogOddsSelected.png
inst/doc/estrogen/MAPlotLabels.png
inst/doc/estrogen/MAplotContrastSelected.png
inst/doc/estrogen/MAplotPres10vsAbs10.png
inst/doc/estrogen/MainWinAfterContrastsComputed.png
inst/doc/estrogen/MainWinLinearModelFitComputed.png
inst/doc/estrogen/MainWindowArraysLoaded.png
inst/doc/estrogen/NormalizeSelected.png
inst/doc/estrogen/NormalizedIntensityBoxPlot.png
inst/doc/estrogen/NormalizedIntensityBoxPlotSelected.png
inst/doc/estrogen/OpenTargetsFileDialog.png
inst/doc/estrogen/OpeningEstrogenTargets.png
inst/doc/estrogen/PlotLabelsForDensity.png
inst/doc/estrogen/PlotTitleAndAxisLabels.png
inst/doc/estrogen/RNATargets.png
inst/doc/estrogen/RNATargetsSelected.png
inst/doc/estrogen/RawIntensityBoxPlot.png
inst/doc/estrogen/RawIntensityBoxPlotSelected.png
inst/doc/estrogen/RawIntensityBoxPlotTitle.png
inst/doc/estrogen/Rgui.png
inst/doc/estrogen/RvsTkrplot.png
inst/doc/estrogen/SaveAsSelected.png
inst/doc/estrogen/SavingEstrogen.png
inst/doc/estrogen/SelectingContrastsForVenn.png
inst/doc/estrogen/SetNamesForVenn.png
inst/doc/estrogen/TargetsFileSelected.png
inst/doc/estrogen/Toptable.png
inst/doc/estrogen/ToptableOptions.png
inst/doc/estrogen/ToptableSelected.png
inst/doc/estrogen/UpDownOrBothForVenn.png
inst/doc/estrogen/VennDiagram.png
inst/doc/estrogen/VennDiagramSelected.png
inst/doc/estrogen/affylmGUImain.png
inst/doc/estrogen/estrogen.html
inst/doc/estrogen/estrogenDir.png
inst/doc/estrogen/heatdiagramPlotTitle.png
inst/doc/estrogen/mainWinAfterNormalization.png
inst/doc/estrogen/qqtPlot.png
inst/doc/estrogen/qqtSelected.png
inst/doc/extract.Rnw
inst/doc/extract.pdf
inst/doc/index.html
inst/doc/input
inst/doc/input/EstrogenTargets.png
inst/doc/input/InputFiles.html
inst/doc/style.css
inst/doc/windowsFocus.html
inst/etc
inst/etc/affylmGUI-menus.txt
inst/etc/recent-files.txt
man
man/ALGchangeLog.Rd
man/affylmGUI.Rd
vignettes
vignettes/affylmGUI.Rnw
vignettes/extract.Rnw
affylmGUI documentation built on May 20, 2017, 9:28 p.m.