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SIMAGE: simulation of DNA-microarray gene expression data.

Casper J Albers·Ritsert C Jansen·Jan Kok·Oscar P Kuipers·Sacha Aft van Hijum
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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.

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AlgorithmsComputer GraphicsComputer SimulationDatabase Management SystemsDatabases, GeneticGene Expression ProfilingInformation Storage and RetrievalModels, GeneticOligonucleotide Array Sequence AnalysisSoftwareUser-Computer InterfaceJournal Article

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Casper J Albers, Ritsert C Jansen, Jan Kok, Oscar P Kuipers, Sacha Aft van Hijum. 2006-04-13. SIMAGE: simulation of DNA-microarray gene expression data.. https://doi.org/10.1186/1471-2105-7-205

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