IsoGene
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 pvalues 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:  20070502 
License:  Free 
Value
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 (onesided and twosided) pvalues using permuations 

BH or BY procedure to adjust pvalues 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 qvalues 

the SAM procedure to obtain a list of significant genes 

SAM plot 

plot of adjusted BH and BY pvalues 

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

plot of pvalues obtained using permutation under increasing or decreasing alternatives 
Author(s)
Lin et al.
Maintainer: Martin Otava <martin.otava@uhasselt.be>
References
Modeling Doseresponse 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 DoseResponse Microarray Experiments: a Comparison of Testing Procedures, Multiplicity, and ResamplingBased Inference, Lin et al. 2007, Stat. App. in Gen. & Mol. Bio., 6(1), article 26.
IsoGene: An R Package for Analyzing Doseresponse 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
.