affylmGUI             package:affylmGUI             R Documentation

_G_r_a_p_h_i_c_a_l _U_s_e_r _I_n_t_e_r_f_a_c_e _f_o_r _t_h_e _l_i_m_m_a _m_i_c_r_o_a_r_r_a_y _p_a_c_k_a_g_e

_D_e_s_c_r_i_p_t_i_o_n:

     Graphical User Interface for Affy analysis using the limma
     microarray package

_U_s_a_g_e:

     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(FileName)
     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()

_A_r_g_u_m_e_n_t_s:

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.

     ...: 

   Align: 

     all: 

      BG: 

 Caption: 

    code: 

ContrastNames: 

contrastParameterizationIndex: 

  export: 

    expr: 

FileName: 

    File: 

GraphAbsoluteDirectory: 

GraphBorder: 

GraphFileName: 

graphFileType: 

GraphRelativeDirectory: 

GraphSaveAs: 

haystack: 

  Height: 

     img: 

includeBoth: 

   index: 

initialfile: 

itemName: 

   list1: 

  needle: 

NumContrasts: 

numContrasts: 

 numSets: 

 p.value: 

parameterName: 

 pkgName: 

     pkg: 

plotFunction: 

plottitle: 

     res: 

    set1: 

    set2: 

    set3: 

  string: 

  tclPkg: 

      tt: 

    view: 

   Width: 

WindowTitle: 

  xlabel: 

  ylabel: 

     fit: 

    coef: 

  number: 

genelist: 

       A: 

      eb: 

adjust.method: 

 sort.by: 

  object: 

 include: 

   names: 

     cex: 

     mar: 

contrastsMatrix: 

contrastsMatrixList: 

       n: 

PointSize: 

     {HTMLplotUsingFunction:arg12}

_D_e_t_a_i_l_s:

     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.

_A_u_t_h_o_r(_s):

     James Wettenhall

