IsoGene: Order-Restricted Inference for Microarray Experiments

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.

Author
Dan Lin, Setia Pramana, Tobias Verbeke and Ziv Shkedy
Date of publication
2015-07-23 12:32:36
Maintainer
Rudradev Sengupta <rudradev.sengupta@uhasselt.be>
License
GPL-3
Version
1.0-24

View on R-Forge

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...

Files in this package

IsoGene/DESCRIPTION
IsoGene/NAMESPACE
IsoGene/NEWS
IsoGene/R
IsoGene/R/IsoBHPlot.R
IsoGene/R/IsoGene1.R
IsoGene/R/IsoGenem.R
IsoGene/R/IsoGenemSAM.R
IsoGene/R/IsoPlot.R
IsoGene/R/IsoRawp.R
IsoGene/R/IsoSAMPlot.R
IsoGene/R/IsoTestBH.R
IsoGene/R/IsoTestSAM.R
IsoGene/R/Isoallfdr.R
IsoGene/R/Isofudge.R
IsoGene/R/IsomaxT.R
IsoGene/R/IsopvaluePlot.R
IsoGene/R/Isoqqstat.R
IsoGene/R/Isoqval.R
IsoGene/data
IsoGene/data/dopamine.rda
IsoGene/data/exampleData.rda
IsoGene/inst
IsoGene/inst/doc
IsoGene/inst/doc/IsoGene.pdf
IsoGene/man
IsoGene/man/IsoBHPlot.Rd
IsoGene/man/IsoGene.package.Rd
IsoGene/man/IsoGene1.Rd
IsoGene/man/IsoGenem.Rd
IsoGene/man/IsoGenemSAM.Rd
IsoGene/man/IsoPlot.Rd
IsoGene/man/IsoRawp.Rd
IsoGene/man/IsoSAMPlot.Rd
IsoGene/man/IsoTestBH.Rd
IsoGene/man/IsoTestSAM.Rd
IsoGene/man/Isoallfdr.Rd
IsoGene/man/Isofudge.Rd
IsoGene/man/IsomaxT.Rd
IsoGene/man/IsopvaluePlot.Rd
IsoGene/man/Isoqqstat.Rd
IsoGene/man/Isoqval.Rd
IsoGene/man/dopamine.Rd
IsoGene/man/exampleData.Rd
IsoGene/vignettes
IsoGene/vignettes/IsoGene.Rnw
IsoGene/vignettes/mybook4.cls
IsoGene/vignettes/psfig.sty
IsoGene/vignettes/pupdn1b.png
IsoGene/vignettes/stat1a.png