Package: IsoGeneGUI
Type: Package
Title: A graphical user interface to conduct a dose-response analysis
        of microarray data
Version: 1.20.0
Date: 2012-03-26
Author: Setia Pramana, Dan Lin, Philippe Haldermans, Tobias Verbeke
Maintainer: Setia Pramana <setia.pramana@ki.se>
Description: The IsoGene Graphical User Interface (IsoGene-GUI) is a user friendly interface of the IsoGene package which is aimed to identify for genes with a monotonic trend in the expression levels with respect to the increasing doses using several test statistics: global likelihood ratio test (E2), Bartholomew 1961, Barlow et al. 1972 and Robertson et al. 1988), Williams (1971, 1972), Marcus (1976), the M (Hu et al. 2005) and the modified M (Lin et al. 2007).  The p-values of the global likelihood ratio test (E2) are obtained using the excat distribution and permutation. The other four test statistics are obtained using permutation . Several p-values adjustment are provided:  Bonferroni, Holm (1979), Hochberg (1988), and Sidak procedures for controlling the family-wise Type I error rate (FWER), and BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2001) procedures are used for controlling the FDR. the inference is based on resampling methods, which control the False Discovery Rate (FDR) (both permutations (Ge et al., 2003) and the Significance Analysis of Microarrays (SAM), Tusher et al., 2001).
Depends: tcltk, tkrplot, IsoGene
Imports: multtest, relimp, WriteXLS,gdata, RColorBrewer, geneplotter
Suggests: RUnit
biocViews: Microarray, DifferentialExpression, GUI
References: Pramana S., Haldermans P., and Verbeke, T. (2012) A User
        Friendly Interface for Analyzing Dose-response Studies in
        Microarray Experiments: The IsoGeneGUI package. A Book Chapter
        in Lin, D., Shkedy, Z., Amaratunga,D., Yekutieli, D and
        Bijnens, L. (Editors), "Modeling of Dose-response Microarray
        Data in Early Drug Development Experiments Using R", Springer.
License: GPL-2
LazyLoad: yes
Collate: about.R adjustment.R browse.R browse2.R CalcStat.R
        ChooseStat.R CVPlot.R diginum.R ExactE2.R ExactE2Val.R exit.R
        get.ResSAM.R getDose.R getExprs.R IsofudgeMod.R IsofudgeMod2.R
        IsoGenemMod.R Isomean.R Isoplot.R IsoPlot.mod.R IsoPlotSldr.R
        IsopvalPlot.R IsopvaluePlot.R IsoqqstatMOD.R IsoRawpMod.R
        IsoGeneGUI.R IsoStat.R IsoTest.R loadDataSet.R MeanDiff.R
        onHelpIsoGene.R IsoGeneGUIHelp.R openFile.R Permutation.R
        PermuteSAM.R Plot2.R PlotFdrDlt.R PlotFPDlt.R PlotSigDlt.R
        printExact.R printsummary.R PvalAdj.R samplot2.R save.result.R
        save.result.mult.R saveDir.R SaveGraph.R saveXls.R savingRwd.R
        SEPlot.R Setseed.R showdata.R Signif.R summ.R UserPlot.R
        UserPlotting.R xfudge.R test_IsoGeneGUI_package.R
        IsoGeneGUIVignette.R
URL: http://www.ibiostat.be/software/IsoGeneGUI/index.html
Packaged: 2014-04-12 05:22:09 UTC; biocbuild
Built: R 3.1.0; ; 2014-04-12 11:31:05 UTC; unix
