The example data in the package comes from a pre-clinical evaluation study of an active compound in microarray setting. The dose-response microarray data contains 1000 genes and 6 doses (0 (control), 0.01, 0.04, 0.16, 0.63, 2.5 mg/kg) with 4-5 arrays at each dose level.
The data set, which has 1000 features and 26 samples, is placed in a workspace called "dopamine2.RDA" . The data is provided inside folder exampleData of the IsoGeneGUI package (will be automatically opened when we choose " File > open dataset > R workspace " in the package).
The "dopamine2" workspace contains two objects: "dose" and "dopamine". The object "dopamine" contains gene expression matrix and the object "dose" provides the dose levels.
References:

- Lin et al. 2007, Testing for Trend in Dose-Response Microarray Experiments: a Comparison of Testing Procedures, Multiplicity, and Resampling-Based Inference. Stat.App. in Gen. & Mol. Bio., 6(1), article 26.
- Goehlmann, H. and Talloen, W. 2009, Gene Expression Studies Using Affymetrix Microarrays, Chapman & Hall/CRC.
- Setia Pramana, Dan Lin, Philippe Haldermans, Ziv Shkedy, Tobias Verbeke, Hinrich Göhlmann, An De Bondt, Willem Talloen, and Luc Bijnens. 2010, Analysis of Dose-response Studies in Microarray Experiments using The R IsoGene Package, R Journal, 2/1.
- Pramana S., Haldermans P., and Verbeke, T. (2012) A User Friendly Interface for Analyzing Dose-response Studies in Microarray Experiments: The IsoGeneGUI package. A Book Chapter in Lin, D., Shkedy, Z., Amaratunga,D., Yekutieli, D and Bijnens, L. (Editors), "Modeling of Dose-response Microarray Data in Early Drug Development Experiments Using R", Springer.

Example Data: Dopamine Study

Home