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.