IsoGeneGUI

A graphical user interface to conduct a dose-response analysis of microarray data

Bioconductor version: Development (3.0)

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).

Author: Setia Pramana, Dan Lin, Philippe Haldermans, Tobias Verbeke

Maintainer: Setia Pramana <setia.pramana at ki.se>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("IsoGeneGUI")

To cite this package in a publication, start R and enter:

    citation("IsoGeneGUI")

Documentation

PDF R Script IsoGeneGUI Vignette
PDF   Reference Manual

Details

biocViews DifferentialExpression, GUI, Microarray, Software
Version 1.21.0
In Bioconductor since BioC 2.7 (R-2.12)
License GPL-2
Depends tcltk, tkrplot, IsoGene
Imports multtest, relimp, WriteXLS, gdata, RColorBrewer, geneplotter
Suggests RUnit
System Requirements
URL http://www.ibiostat.be/software/IsoGeneGUI/index.html
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source IsoGeneGUI_1.21.0.tar.gz
Windows Binary IsoGeneGUI_1.21.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) IsoGeneGUI_1.21.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center