SIMAGE: simulation of DNA-microarray gene expression data.
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.


CONCLUSIONS
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.
Albers
Casper J
CJ
Groningen Bioinformatics Centre, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, The Netherlands. c.j.albers@open.ac.uk
Jansen
Ritsert C
RC
Kok
Jan
J
Kuipers
Oscar P
OP
van Hijum
Sacha Aft
SA
D000465:Algorithms; D003196:Computer Graphics; D003198:Computer Simulation; D003628:Database Management Systems; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012984:Software; D014584:User-Computer Interface