The IsoGene Project
The IsoGene Project is a project aimed for developing methodology and software to perform analysis of dose-response microarray studies. The methodology and software implementation are described in the book "Modeling dose-response microarray data in early drug development using R". The book covers the following topics:
- Estimation and inference under order constrains.
- Parametric modeling of dose-response microarray data.
- Multiplicity adjustment.
- Permutation test and resampling based inference and multiple testing.
- Significance analysis if dose-response microarray data (SAM)
- Order restricted clustering.
- Classification genes based on information criteria.
- Hierarchical Bayesian approach.
- Model based approach for dose-response microarray data.
- Model averaging.
- Multiple test contrasts.
- Ratio tests.
- FDR adjusted confidence intervals for selected parameters
Software
Two packages in R were developed in this project:
- The IsoGene package is a command based package in R in which all the methodology is implemented.
- The Graphical User Interface (IsoGeneGUI) is a user friendly interface of the IsoGene package which is developed for the user with no or limited knowledge about R. The IsoGeneGUI was developed using tcl/tk.
In addition to IsoGene and IsoGeneGUI various R packages are applied for specific settings, which include nlme, multtest, ORCM, MLP, BRUGs, MCPMod, DoseFinding, multcomp and mratios. The working assumption is that the users have a basic knowledge of R and therefore complete working examples are provided for the data analyzes presented in the book. Readers with very limited knowledge of R that wish to perform the analyzes presented in the book can do it easily using the IsoGeneGUI which does not require knowledge in R syntax.
Project developers
Marc Aerts, Dhammika Amaratunga, Janine Arts, Luc Bijnens, An De Bondt, Tomasz Burzykowski, Djork-Arné Clevert, Filip De Ridder, Gemechis Dijta Dilba, Hinrich Göhlmann, Philippe Haldermans, Sepp Hochreiter, Ludwig Hothorn, Adetayo Kasim, Bernet Kato, Dan Lin, Pieter Peeters, Tim Perrera, Setia Pramana, Nandini Raghavan, Ziv Shkedy, Roel Straetemans, Willem Talloen, Tobias Verbeke and Dani Yekutieli.
Software developers
Dan Lin, Tobias Verbeke, Setia Pramana, Philippe Haldermans.
Website developer
Setia Pramana
