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IsoGene (version 1.0-24)

Order-Restricted Inference for Microarray Experiments

Description

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.

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Version

Install

install.packages('IsoGene')

Monthly Downloads

139

Version

1.0-24

License

GPL-3

Last Published

July 31st, 2015

Functions in IsoGene (1.0-24)

IsomaxT

The maxT procedure for order restricted inference
Isoallfdr

Obtaining the delta table in the SAM procedure
IsoGenemSAM

The five SAM test statistics calculated for both the increasing and decreasing trends
IsoGenem

The five test statistics calculated for both the increasing and decreasing trends
exampleData

Dose-response microarray example data
dopamine

Dose-response microarray example data
IsoGene1

The five test statistics calculated for both the increasing and decreasing trends
IsoBHPlot

Plot of adjusted p-values using BH or BY adjustment
Isofudge

Calculation of the fudge factor for the five SAM test statistics in the SAM procedure
IsoGene-package

IsoGene
Isoqqstat

Implementation of five SAM test statistics in the SAM procedure
IsoTestBH

Test of monotonic trends using the five test statistics with BH or BY adjustment
IsopvaluePlot

Plot of p-values from permutations under increasing or decreasing alternatives
IsoSAMPlot

Plots produced using the SAM procedure
Isoqval

Obtaining the list of significant genes using the SAM procedure
IsoTestSAM

Obtaining the list of significant genes using the SAM procedure
IsoPlot

IsoPlot
IsoRawp

IsoRawp