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affy (version 1.50.0)

affylmGUI: Graphical User Interface for the limma microarray package

Description

Graphical User Interface for Affy analysis using the limma microarray package

Usage

AboutaffylmGUI()
affyHelp()
affylmGUI(BigfontsForaffylmGUIpresentation=FALSE)
affylmGUIhelp()
affyPlotMA()
affyPlotMAcontrast()
ALGlimmaUsersGuide(view=TRUE)
ChooseCDF()
ChooseContrastParameterization()
chooseDir()
ChooseEbayesStatistic()
ComputeContrasts()
ComputeLinearModelFit()
CopyGraph(img)
DeleteContrastParameterization()
deleteItemFromList(list1,itemName=NULL,index=NULL)
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 = .HTML.file, 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(n = 20)
showCitations()
showTopTable(...,export=FALSE)
SimplifyContrastsExpression(string)
strstr(haystack, needle)
tclArrayVar()
TclRequire(tclPkg)
topTable2(fit, coef = 1, number = 10, genelist = NULL,adjust.method = "holm", sort.by = "B")
toptable2(fit, coef = 1, number = 10, genelist = NULL, A = NULL,eb = NULL, adjust.method = "holm", sort.by = "B", ...)
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

BigfontsForaffylmGUIpresentation
affylmGUI:arg1:If set to TRUE, 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.
...
HTMLplotUsingFunction:arg14:and:showTopTable:arg1:and:toptable2:arg9: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
index
deleteItemFromList:arg3:an index
initialfile
SetupPlotMenus:arg2:and:SaveGraphAsJpeg:arg1:and:SaveGraphAsPDF:arg1:and:SaveGraphAsPNG:arg1:and:SaveGraphAsPostscript:arg1
itemName
deleteItemFromList:arg2:an item name
list1
deleteItemFromList:arg1:a list
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
view
ALGlimmaUsersGuide:arg1:A boolean determinig if the users'd guide will be viewed
Width
HTMLplotUsingFunction:arg10
WindowTitle
generalPlotFunction: arg2: a title
xlabel
GetPlotLabels:arg2
ylabel
GetPlotLabels:arg3
fit
topTable2:arg1:and:toptable2:arg1
coef
topTable2:arg2:and:toptable2:arg2
number
topTable2:arg3:and:toptable2:arg3
genelist
topTable2:arg4:and:toptable2:arg4
A
toptable2:arg5
eb
toptable2:arg6
adjust.method
topTable2:arg5:and:toptable2:arg7
sort.by
topTable2:arg6:and:toptable2:arg8
object
vennDiagramaffylmGUI:arg1
include
vennDiagramaffylmGUI:arg2
names
vennDiagramaffylmGUI:arg3
cex
vennDiagramaffylmGUI:arg4
mar
vennDiagramaffylmGUI:arg5
contrastsMatrix
ViewContrastsMatrixAsPairs:arg1
contrastsMatrixList
ViewContrastsMatrixAsPairs:arg2:and:ViewContrastsMatrixInTable:arg1
n
showChangeLog:arg1
PointSize
HTMLplotUsingFunction:arg12

Details

This function launches a Graphical User Interface for the limma package by Gordon Smyth. The GUI uses Tk widgets (via the R TclTk interface by Peter Dalgaard) in order to provide a simple interface to the limma functions for linear modelling of microarrays and identification of differentially expressed genes.