IsoGene

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Description

Library IsoGene aims to identify for genes with a monotonic trend in the expression levels with respect to the increasing doses using several test statistics. They include the global likelihood ratio test (E^2, 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 five test statistics are obtained using permutation and they are adjusted using BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2004) procedures are used for controlling the FDR.

Details

Package: IsoGene
Type: Package
Version: 1.0
Date: 2007-05-02
License: Free

Value

The package includes the following functions:

IsoGene1

calculates the five test statistics in testing both increasing and decreasing alternatives for a single gene

IsoGenem

calculates the five test statistics in testing both increasing and decreasing alternatives for all the genes in the data set

IsoRawp

obtains the raw (one-sided and two-sided) p-values using permuations

IsoTestBH

BH or BY procedure to adjust p-values while controlling FDR

IsoGenemSAM

calculates the SAM test statistic

Isofudge

calculates the fudge factor in the SAM test statistic

Isoqqstat

calculates the SAM test statistic using permutations

Isoallfdr

obtains the delta table in the SAM procedure

Isoqval

the SAM procedure to obtain q-values

IsoTestSAM

the SAM procedure to obtain a list of significant genes

IsoSAMPlot

SAM plot

IsoBHPlot

plot of adjusted BH and BY p-values

IsoPlot

plot of data, sample means, and a fitted isotonic regression curve with a likely direction

IsopvaluePlot

plot of p-values obtained using permutation under increasing or decreasing alternatives

Author(s)

Lin et al.

Maintainer: Martin Otava <martin.otava@uhasselt.be>

References

Modeling Dose-response Microarray Data in Early Drug Development Experiments Using R, Lin D., Shkedy Z., Yekutieli D., Amaratunga D., and Bijnens, L. (editors), (2012), Springer.

Testing for Trend in Dose-Response Microarray Experiments: a Comparison of Testing Procedures, Multiplicity, and Resampling-Based Inference, Lin et al. 2007, Stat. App. in Gen. & Mol. Bio., 6(1), article 26.

IsoGene: An R Package for Analyzing Dose-response Studies in Microarray Experiments, Pramana S., Lin D., Haldermans P., Shkedy Z., Verbeke T., De Bondt A., Talloen W., Goehlmann H., Bijnens L. 2010, R Journal 2/1.

See Also

mt.rawp2adjp, IsoGene1, IsoGenem,IsoRawp, IsoTestBH, IsoGenemSAM, Isofudge, Isoqqstat,Isoallfdr,Isoqval,IsoTestSAM, IsoSAMPlot, IsoBHPlot, IsoPlot.