affylmGUI: GUI for limma package with Affymetrix microarrays

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

AuthorJames Wettenhall [aut], Ken Simpson [aut], Gordon Smyth [aut], Keith Satterley [ctb], Yifang Hu [ctb]
Date of publicationNone
MaintainerYifang Hu <hu@wehi.edu.au>, Gordon Smyth <smyth@wehi.edu.au>, Keith Satterley <keith@wehi.edu.au>
LicenseGPL (>=2)
Version1.48.0
http://bioinf.wehi.edu.au/affylmGUI/

View on Bioconductor

Functions

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

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.