Package 'affylmGUI'

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

Description

The affylmGUI package provides a Graphical User Interface (GUI) for analysis of Affymetrix microarray data using the limma package (Linear Modes for MicroArray data).

Details

The GUI is launched by typing affylmGUI() at the R prompt. For detailed help, including example sesssions, see the affylmGUI home page at http://bioinf.wehi.edu.au/affylmGUI.

The limma package offers R users a command-line interface to state-of-the-art techniques for linear modelling of microarray data and for identifying differentially expressed genes (Ritchie et al, 2015). The affylmGUI package, while not as powerful as limma to the expert user, offers a simple point-and-click interface to many of the commonly-used limma and affy functions.

To use the affylmGUI package, you need to have R 1.8.1 or later, Tcl/Tk 8.3 or later (ActiveTcl for Windows/Linux or Fink Tcl/Tk for MacOSX (X11)) and the limma, affylmGUI and tkrplot R packages. At least one of the affy, gcrma or affyPLM Bioconductor packages are also required for normalization and probe-set summarization. The R2HTML (CRAN) and xtable (CRAN) packages are recommended. affylmGUI has been tested succesfully on Windows, Red Hat Linux, and on Mac OSX with X11.

Please cite Wettenhall et al (2006) if you use results from affylmGUI in a publication. Also consider citing Irizarry et al (2003) if RMA normalization is used for Wu et al (2004) if gcrma normalization is used.

Author(s)

Created by James Wettenhall between 2003 and September 2006. Maintained by Keith Satterley between September 2006 and July 2015. Currently maintained by Gordon Smyth.

References

Wettenhall, JM, Simpson, KM, Satterley, K, Smyth, GK (2006). affylmGUI: a graphical user interface for linear modeling of single channel microarray data. Bioinformatics 22, 897-899.

Ritchie, ME, Phipson, B, Wu, D, Hu, Y, Law, CW, Shi, W, and Smyth, GK (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research 43, e47. http://nar.oxfordjournals.org/content/43/7/e47

Irizarry, RA, Hobbs, B, Collin, F, Beazer-Barclay, YD, Antonellis, KJ, Scherf, U, Speed, TP (2003). Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4(2), 249-264.

Wu, Z, Irizarry, RA, Gentleman, R, Martinez-Murillo, F, Spencer, F. (2004). A model based background adjustment for oligonucleotide expression arrays. Journal of the American Statistical Association 99(468), 909-917.

See Also

The GUI is launched by affylmGUI().

More documentation is available from http://bioinf.wehi.edu.au/affylmGUI.

showChangeLog() shows the most recent lines from the affylmGUI package changeLog.

See limma-package for help about the limma package.

Examples

library(limma)
changeLog(package="affylmGUI")

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Graphical User Interface for the limma microarray package

Description

Graphical User Interface for limma package analysis of Affymetrix microarrays.

Usage

affylmGUI(BigfontsForaffylmGUIpresentation=FALSE)

Arguments

BigfontsForaffylmGUIpresentation

logical, if TRUE then larger fonts are used. However, some font sizes are not controlled by affylmGUI and so must be adjusted in the operating system, e.g., in the Control Panel in Windows under Display, Appearance.

Details

The affylmGUI function launches a Graphical User Interface for the affy, gcrma, affyPLM and limma packages. The GUI uses Tk widgets (via the R TclTk interface by Peter Dalgaard) in order to provide a simple interface to limma functions for linear modelling of Affymetrix microarrays and identification of differentially expressed genes.

Almost all users will type affylmGUI(). The use of affylmGUI(Bigfonts=TRUE) is only intended for the preparation of a talk about the affylmGUI package.

Author(s)

Created by James Wettenhall between 2003 and September 2006. Maintained by Keith Satterley between September 2006 and July 2015. Currently maintained by Gordon Smyth.

See Also

affylmGUI-package, internal

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Internal Functions

Description

Internal functions defined by the affylmGUI package.

Usage

AboutaffylmGUI()
affyHelp()
affylmGUIhelp()
affyPlotMA()
affyPlotMAcontrast()
ChooseCDF()
ChooseContrastParameterization()
chooseDir()
ChooseEbayesStatistic()
ComputeContrasts()
ComputeLinearModelFit()
CopyGraph(img)
DeleteContrastParameterization()
DensityPlot()
DensityPlotAll()
evalRcode()
ExportHTMLreport()
ExportNormalizedExpressionValues()
ExportTopTable()
fixSeps(string)
generalPlotFunction(code="",WindowTitle="")
GetComponentsToExportInHTMLreport(contrastParameterizationIndex=NULL)
GetContrast(contrastParameterizationIndex)
GetContrastNamesForHeatDiagram(numContrasts=2,ContrastNames=c("Contrast 1","Contrast 2"))
GetContrastParameterizationName()
GetContrasts(NumContrasts=0)
GetDEcutoff()
GetGeneLabelsOptions()
GetJpegOrPngParams(graphFileType)
GetJpegOrPngX11Params(graphFileType)
GetlimmaDataSetName()
GetLogPLMDataChoice()
GetMultipleContrasts(contrastParameterizationIndex)
GetNormalizationMethod()
getPackageVersion(pkgName)
GetParameterizationName()
GetPlotLabels(plottitle="",xlabel="",ylabel="")
GetPlotSize()
GetPlotTitle(plottitle="")
GetPValueCutoff(p.value=0.01)
GetResidualTypeChoice()
GetRNATypesFrom.ContrastsFromDropDowns.String(string)
GetSetNames(numSets=2,set1="",set2="",set3="")
GetSlideNum(all=FALSE)
GetSlideNums()
GetWhichProbes(includeBoth=FALSE)
GetWtAreaParams()
GetWtFlagParams()
HeatDiagramDialog(parameterName)
HeatDiagramPlot()
HTMLplotUsingFunction(Caption = "", File = "plot.html", GraphRelativeDirectory = ".", GraphAbsoluteDirectory = NULL, GraphFileName = "", GraphSaveAs = "png", GraphBorder = 1,  Align = "center", plotFunction = NULL,Width=600,Height=600,PointSize=12,BG="white",res=72,...)
ImageArrayPlot()
ImageQualityResidualPlot()
ImageQualityWeightPlot()
initGlobals()
IntensityHistogram()
IntensityHistogramAll()
limmaHelp()
LogOddsPlot()
NewLimmaFile()
NormalizedIntensityBoxPlot()
NormalizeNow()
nstrstr(haystack,needle)
NUSEPlotAll()
onDestroy()
onExit()
OpenALimmaFile(FileName)
OpenCDFandTargetsfiles()
OpenCDFFile()
OpenLimmaFile()
OpenTargetsFile()
PlotOptions()
QQTplot()
RawIntensityBoxPlot()
Require(pkg)
Resize(img,plotFunction)
RLEPlotAll()
RNADegradationPlotAll()
SaveAsLimmaFile()
SaveGraphAsJpeg(initialfile, plotFunction)
SaveGraphAsPDF(initialfile, plotFunction)
SaveGraphAsPNG(initialfile, plotFunction)
SaveGraphAsPostscript(initialfile, plotFunction)
SaveLimmaFile()
SetupPlotKeyBindings(tt,img)
SetupPlotMenus(tt,initialfile,plotFunction,img)
SetWD()
showChangeLog()
showCitations()
showTopTable(...,export=FALSE)
SimplifyContrastsExpression(string)
strstr(haystack, needle)
tclArrayVar()
TclRequire(tclPkg)
Try(expr)
TryReadImgProcFile(expr)
UpDownOrBoth()
vennDiagramaffylmGUI(object, include = "both", names, cex = 1.5, mar = rep(1, 4), ...)
VennDiagramPlot()
ViewContrastsMatrixAsPairs(contrastsMatrix, contrastsMatrixList,contrastParameterizationIndex = NULL)
ViewContrastsMatrixInTable(contrastsMatrixList, contrastParameterizationIndex = NULL)
ViewExistingContrastParameterization()
ViewRNATargets()

Arguments

...	HTMLplotUsingFunction:arg14:and:showTopTable:arg1:and:vennDiagramaffylmGUI:arg6
Align	HTMLplotUsingFunction:arg8
all	GetSlideNum:arg1
BG	HTMLplotUsingFunction:arg12
Caption	HTMLplotUsingFunction:arg1
code	generalPlotFunction: arg1: a code
ContrastNames	GetContrastNamesForHeatDiagram:arg2
contrastParameterizationIndex	GetComponentsToExportInHTMLreport:arg1:and:contrastParameterizationIndex:arg1:and:GetContrast:arg1:and:HTMLplotUsingFunction:arg3:and:ViewContrastsMatrixInTable:arg2
export	showTopTable:arg2
expr	Try:arg1:and:TryReadImgProcFile:arg1
File	HTMLplotUsingFunction:arg2
FileName	OpenALimmaFile:arg1
GraphAbsoluteDirectory	HTMLplotUsingFunction:arg4
GraphBorder	HTMLplotUsingFunction:arg7
GraphFileName	HTMLplotUsingFunction:arg5
graphFileType	GetJpegOrPngParams:arg1:and:GetJpegOrPngX11Params:arg1
GraphRelativeDirectory	HTMLplotUsingFunction:arg3
GraphSaveAs	HTMLplotUsingFunction:arg6
haystack	nstrstr:arg1:and:strstr:arg1
Height	HTMLplotUsingFunction:arg11
img	Resize:arg1:and:SetupPlotMenus:arg4:and:CopyGraph:arg1:and:SetupPlotKeyBindings:arg2
includeBoth	GetWhichProbes:arg1
initialfile	SetupPlotMenus:arg2:and:SaveGraphAsJpeg:arg1:and:SaveGraphAsPDF:arg1:and:SaveGraphAsPNG:arg1:and:SaveGraphAsPostscript:arg1
needle	nstrstr:arg2:and:strstr:arg2
NumContrasts	GetContrasts:arg1
numContrasts	GetContrastNamesForHeatDiagram:arg1
numSets	GetSetNames:arg1
p.value	GetPValueCutoff:arg1:A p-value cutoff.
parameterName	HeatDiagramDialog:arg1
pkgName	getPackageVersion:arg1
pkg	Require:arg1
plotFunction	Resize:arg2:and:HTMLplotUsingFunction:arg9:and:SetupPlotMenus:arg3:and:SaveGraphAsJpeg:arg2:and:SaveGraphAsPDF:arg2:and:SaveGraphAsPNG:arg2:and:SaveGraphAsPostscript:arg2
plottitle	GetPlotLabels:arg1:and:GetPlotTitle:arg1
res	HTMLplotUsingFunction:arg13
set1	GetSetNames:arg2
set2	GetSetNames:arg3
set3	GetSetNames:arg4
string	fixSeps:arg1:A character string:and:GetRNATypesFrom.ContrastsFromDropDowns.String:arg1:and:SimplifyContrastsExpression:arg1
tclPkg	TclRequire:arg1
tt	SetupPlotMenus:arg1:and:SetupPlotKeyBindings:arg1
Width	HTMLplotUsingFunction:arg10
WindowTitle	generalPlotFunction: arg2: a title
xlabel	GetPlotLabels:arg2
ylabel	GetPlotLabels:arg3
object	vennDiagramaffylmGUI:arg1
include	vennDiagramaffylmGUI:arg2
names	vennDiagramaffylmGUI:arg3
cex	vennDiagramaffylmGUI:arg4
mar	vennDiagramaffylmGUI:arg5
contrastsMatrix	ViewContrastsMatrixAsPairs:arg1
contrastsMatrixList	ViewContrastsMatrixAsPairs:arg2:and:ViewContrastsMatrixInTable:arg1
PointSize	HTMLplotUsingFunction:arg12

Details

These functions are called by affylmGUI() via the GUI and are not intended to be called directly by users.

Author(s)

Created by James Wettenhall between 2003 and September 2006. Maintained by Keith Satterley between September 2006 and July 2015. Currently maintained by Gordon Smyth.

See Also

affylmGUI

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