IsoGene.package: IsoGene

Description Details Value Author(s) References See Also


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.


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


The package includes the following functions:


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


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


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


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


calculates the SAM test statistic


calculates the fudge factor in the SAM test statistic


calculates the SAM test statistic using permutations


obtains the delta table in the SAM procedure


the SAM procedure to obtain q-values


the SAM procedure to obtain a list of significant genes


SAM plot


plot of adjusted BH and BY p-values


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


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


Lin et al.

Maintainer: Martin Otava <>


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.

IsoGene documentation built on May 29, 2017, 1:53 p.m.

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