limmaGUI              package:limmaGUI              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 the limma microarray package

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

     limmaGUI()
     GetComponentsToExportInHTMLreport()
     HTMLplotUsingFunction()
     ExportTopTable()
     ExportHTMLreport()
     TryReadImgProcFile()
     Require()
     TclRequire()
     getPackageVersion()
     initGlobals()
     deleteItemFromList()
     SetLayoutParameters()
     OpenGALFile()
     OpenTargetsFile()
     OpenSpotTypesFile()
     GetImageProcessingFileType()
     ReadImageProcessingFiles()
     tclArrayVar()
     GetDesignOrContrasts()
     SimplifyContrastsExpression()
     GetRNATypesFrom.ContrastsFromDropDowns.String()
     GetParameterNames()
     GetReducedDuplicateSpacing()
     GetContrastsParameterizationNames()
     GetSpotTypesIncludedNames()
     HowManyDups()
     ViewDesignOrContrastsMatrixInTable()
     ViewDesignOrContrastsMatrixAsPairs()
     ViewExistingContrastsParameterization()
     ViewExistingParameterization()
     CreateNewParameterization()
     ViewRNATargets()
     nstrstr()
     strstr()
     ViewSpotTypes()
     ComputeContrasts()
     ComputeLinearModel()
     ChooseParameterization()
     GetCoef()
     showTopTable()
     GetSpotTypesForLinearModel()
     GetSlideNum()
     GetDEcutoff()
     UpdateSpotTypesStatus()
     ChooseEbayesStatistic()
     ChooseSpotType()
     GetWtAreaParams()
     GetWtFlagParams()
     evalRcode()
     OpenGALandTargetsandSpotTypesfiles()
     GetlimmaDataSetName()
     GetParameterizationName()
     GetContrastsParameterizationName()
     ImportMA()
     ImportMADialog()
     NewLimmaFile()
     SetWD()
     onExit()
     DeleteParameterization()
     ChooseContrastsParameterization()
     DeleteContrastsParameterization()
     OpenLimmaFile()
     OpenALimmaFile(FileName)
     SaveLimmaFile()
     SaveAsLimmaFile()
     AboutLimmaGUI()
     addMenuItem()
     GetMenuName()
     GetNumParametersNoTargets()
     AboutCustomMenu()
     DeleteCustomMenuItem()
     GetCustomMenuItemNum()
     GetWithinArrayNormalizationMethod()
     GetBetweenArrayNormalizationMethod()
     NormalizeNow()
     AboutNormalization()
     GetGeneLabelsOptions()
     MAPlotAvg()
     MMPlot()
     GetParametersAndOrContrasts()
     HeatDiagramDialog()
     HeatDiagramPlot()
     ImageArrayPlotDialog()
     ImageArrayPlot()
     LogOddsPlot()
     DupCorBoxPlot()
     QQTplot()
     MBoxPlot()
     PrintTipGroupMAPlot()
     MAPlot()
     ChoosePlotSymbolByClicking()
     SelectPlotSymbols()
     plotMAColorCoded()
     GetNEWxlim()
     ebayesBoxPlots()
     GetPlotLabels()
     GetPlotTitle()
     GetPlotSize()
     read.marrayTools(MFile,AFile, path, verbose, sep, quote, header, ...)
     Resize()
     SaveGraphAsJpeg()
     SaveGraphAsPNG()
     SaveGraphAsPostscript()
     SaveGraphAsPDF()
     showGAL()
     CopyGraph()
     SetupPlotKeyBindings()
     SetupPlotMenus()
     GetJpegOrPngParams()
     GetJpegOrPngX11Params()
     VennDiagramPlot()
     UpDownOrBoth()
     GetBackgroundCorrectionMethod()
     GetlmFitMethod()
     lmFitMethodHelp()
     BChelp()
     fixSeps(string)
     limmaHelp()
     limmaUsersGuide()
     showCitations()
     showChangeLog()
     onDestroy()
     limmaGUI(BigfontsForlimmaGUIpresentation=FALSE)
     GetPValueCutoff(p.value=0.01)
     GetImageAnalysisColumnHeadings()
     GetLowessType()
     PlotOptions()

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

BigfontsForlimmaGUIpresentation: If set to TRUE, larger fonts are used.
           However, some font sizes are not controlled by limmaGUI and
          so must be adjusted in the operating system, e.g. in the
          Control Panel in Windows under Display, Appearance.

   MFile: Flat-file of log-ratios output by marrayTools

   AFile: Flat-file of log-intensities output by marrayTools

    path: Path to the directory containing the MFile and AFile

 verbose: Optional diagnostic messages

     sep: Column separator. ("\t" for tab-delimited text)

   quote: See help for read.table

  header: See help for read.table

 p.value: A p-value cutoff.

FileName: A file name.

  string: A character string.

     ...: Any other arguments to read.marrayTools are passed to
          'read.table'

_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

