Software

SIMAGE: simulation of DNA-microarray gene expression data

Casper J Albers^1,3* , Ritsert C Jansen¹ , Jan Kok² , Oscar P Kuipers² and Sacha AFT van Hijum^2*

¹  Groningen Bioinformatics Centre, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, The Netherlands

²  Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, The Netherlands

³  Department of Statistics, The Open University, Walton Hall, Milton Keynes MK7 6AA, UK

author email corresponding author email* Contributed equally

BMC Bioinformatics 2006, 7:205doi:10.1186/1471-2105-7-205

Published:	13 April 2006

Abstract

Background

Simulation of DNA-microarray data serves at least three purposes: (i) optimizing the design of an intended DNA microarray experiment, (ii) comparing existing pre-processing and processing methods for best analysis of a given DNA microarray experiment, (iii) educating students, lab-workers and other researchers by making them aware of the many factors influencing DNA microarray experiments.

Results

Our model has multiple layers of factors influencing the experiment. The relative influence of such factors can differ significantly between labs, experiments within labs, etc. Therefore, we have added a module to roughly estimate their parameters from a given data set. This guarantees that our simulated data mimics real data as closely as possible.

Conclusion

We introduce a model for the simulation of dual-dye cDNA-microarray data closely resembling real data and coin the model and its software implementation "SIMAGE" which stands for simulation of microarray gene expression data. The software is freely accessible at: http://bioinformatics.biol.rug.nl/websoftware/simage webcite.