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

