IsoGene: An R Package for Analyzing Dose-response Studies in Microarray Experiments

Authors

Setia Pramana, Universiteit Hasselt
Dan Lin, Universiteit Hasselt
Philippe Haldermans, Universiteit Hasselt
Ziv Shkedy, Universiteit Hasselt
Tobias Verbeke, OpenAnalytics BVBA
Hinrich Göhlmann, Johnson and Johnson Pharmaceutical Research and Development, a division of Janssen Pharmaceutica
An De Bondt, Johnson and Johnson Pharmaceutical Research and Development, a division of Janssen Pharmaceutica
Williem Talloen, Johnson and Johnson Pharmaceutical Research and Development, a division of Janssen Pharmaceutica
Luc Bijnens, Johnson and Johnson Pharmaceutical Research and Development, a division of Janssen Pharmaceutica

Date of this Version

6-2010

Document Type

Article

Citation

The R Journal (June 2010) 2(1)

Comments

Copyright 2010, The R Foundation. Open access material. License: CC BY 3.0 Unported

Abstract

IsoGene is an R package for the analysis of dose-response microarray experiments to identify gene or subsets of genes with a mono tone relationship between the gene expression and the doses. Several testing procedures (i.e., the likelihood ratio test, Williams, Marcus, the M, and Modified M), that take into account the order restriction of the means with respect to the increasing doses are implemented in the package. The inference is based on resampling methods, both permutations and the Significance Analysis of Microarrays (SAM).