SIMAGE: simulation of DNA-microarray gene expression data.

BMC Bioinformatics
Casper J AlbersSacha Aft van Hijum

Abstract

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. 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. 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.

References

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Citations

Aug 10, 2007·Nature Biotechnology·Chris F TaylorHenning Hermjakob
Apr 12, 2008·Nucleosides, Nucleotides & Nucleic Acids·Karsten SiegmundClemens Richert
Feb 17, 2009·BMC Bioinformatics·Monica ChiognaChiara Romualdi
Aug 21, 2013·Bioinformatics·Robert MaierRobert Küffner
Oct 17, 2006·Molecular Microbiology·Sigrid C J De KeersmaeckerKathleen Marchal
Jan 1, 2015·Microarrays·Farhad Maleki, Anthony Kusalik
Jul 23, 2021·Journal of Bioinformatics and Computational Biology·Shiguo DengHuijie Yang

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Datasets Mentioned

BETA
GDS273
MEXP-225

Methods Mentioned

BETA
saturation Slide
chips
chip

Software Mentioned

FreePascal
MolGen
MathType
Apache
SIMAGE
R
ArrayExpress

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