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.
- Göhlmann,
H. W. 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 W.H.
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