Package: IsoGeneGUI
Type: Package
Title: A graphical user interface to conduct a dose-response analysis
        of microarray data
Version: 1.2.1
Date: 2009-11-16
Author: Setia Pramana, Dan Lin, Philippe Haldermans, Tobias Verbeke
Maintainer: Setia Pramana <setia.pramana@uhasselt.be>
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, Statistics, DifferentialExpression, GUI
References: Lin, D., Shkedy, Z., Yekutieli, D., Burzykowski, T.,
        Gohlmann, H., De Bondt, A., Perera, T., Geerts, T. and Bijnens,
        L. (2007) Testing for trends in dose-response microarray
        experiments: A comparison of several testing procedures,
        multiplicity and resampling-based inference. Statistical
        Applications in Genetics and Molecular Biology, 6(1), Article
        26.
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
URL: http://www.ibiostat.be/software/IsoGeneGUI/index.html
Packaged: 2010-12-12 13:22:35 UTC; biocbuild
Built: R 2.12.0; ; 2010-12-12 17:48:46 UTC; unix
