IsoGene: Order-Restricted Inference for Microarray Experiments
Version 1.0-24

Offers framework for testing for monotonic relationship between gene expression and doses in a microarray experiment. Several testing procedures including the global likelihood-ratio test (Bartholomew, 1961), Williams (1971, 1972), Marcus (1976), M (Hu et al. 2005) and the modified M (Lin et al. 2007) are used to test for the monotonic trend in gene expression with respect to doses. BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2004) FDR controlling procedures are applied to adjust the raw p-values obtained from the permutations.

AuthorDan Lin, Setia Pramana, Tobias Verbeke and Ziv Shkedy
Date of publication2015-07-31 12:11:58
MaintainerRudradev Sengupta <rudradev.sengupta@uhasselt.be>
LicenseGPL-3
Version1.0-24
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("IsoGene")

Popular man pages

dopamine: Dose-response microarray example data
Isoallfdr: Obtaining the delta table in the SAM procedure
Isofudge: Calculation of the fudge factor for the five SAM test...
IsoGenemSAM: The five SAM test statistics calculated for both the...
IsoGene.package: IsoGene
IsoPlot: IsoPlot
IsopvaluePlot: Plot of p-values from permutations under increasing or...
See all...

All man pages Function index File listing

Man pages

dopamine: Dose-response microarray example data
exampleData: Dose-response microarray example data
Isoallfdr: Obtaining the delta table in the SAM procedure
IsoBHPlot: Plot of adjusted p-values using BH or BY adjustment
Isofudge: Calculation of the fudge factor for the five SAM test...
IsoGene1: The five test statistics calculated for both the increasing...
IsoGenem: The five test statistics calculated for both the increasing...
IsoGenemSAM: The five SAM test statistics calculated for both the...
IsoGene.package: IsoGene
IsomaxT: The maxT procedure for order restricted inference
IsoPlot: IsoPlot
IsopvaluePlot: Plot of p-values from permutations under increasing or...
Isoqqstat: Implementation of five SAM test statistics in the SAM...
Isoqval: Obtaining the list of significant genes using the SAM...
IsoRawp: IsoRawp
IsoSAMPlot: Plots produced using the SAM procedure
IsoTestBH: Test of monotonic trends using the five test statistics with...
IsoTestSAM: Obtaining the list of significant genes using the SAM...

Functions

IsoBHPlot Man page Source code
IsoGene Man page
IsoGene-package Man page
IsoGene1 Man page Source code
IsoGenem Man page Source code
IsoGenemSAM Man page Source code
IsoPlot Man page Source code
IsoRawp Man page Source code
IsoSAMPlot Man page Source code
IsoTestBH Man page Source code
IsoTestSAM Man page Source code
Isoallfdr Man page Source code
Isofudge Man page Source code
IsomaxT Man page Source code
IsopvaluePlot Man page Source code
Isoqqstat Man page Source code
Isoqval Man page Source code
dopamine Man page
exampleData Man page
xfudge Source code

Files

inst
inst/doc
inst/doc/IsoGene.pdf
NAMESPACE
NEWS
data
data/exampleData.rda
data/dopamine.rda
R
R/IsoSAMPlot.R
R/IsoPlot.R
R/IsoTestBH.R
R/IsoGenem.R
R/Isofudge.R
R/IsoGenemSAM.R
R/IsomaxT.R
R/Isoqval.R
R/IsopvaluePlot.R
R/Isoqqstat.R
R/IsoBHPlot.R
R/IsoRawp.R
R/Isoallfdr.R
R/IsoGene1.R
R/IsoTestSAM.R
vignettes
vignettes/mybook4.cls
vignettes/stat1a.png
vignettes/pupdn1b.png
vignettes/psfig.sty
vignettes/IsoGene.Rnw
MD5
DESCRIPTION
man
man/exampleData.Rd
man/Isofudge.Rd
man/IsoTestBH.Rd
man/IsoTestSAM.Rd
man/IsoSAMPlot.Rd
man/IsoGene1.Rd
man/Isoqqstat.Rd
man/IsoGene.package.Rd
man/IsoRawp.Rd
man/Isoqval.Rd
man/IsoGenemSAM.Rd
man/Isoallfdr.Rd
man/IsoGenem.Rd
man/IsopvaluePlot.Rd
man/dopamine.Rd
man/IsoBHPlot.Rd
man/IsomaxT.Rd
man/IsoPlot.Rd
IsoGene documentation built on May 19, 2017, 11:14 a.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.