SIMAGE：DNA微阵列基因表达数据模拟
SIMAGE: simulation of DNA-microarray gene expression data.
作者信息
Albers Casper J, Jansen Ritsert C, Kok Jan, Kuipers Oscar P, van Hijum Sacha Aft
机构信息
Groningen Bioinformatics Centre, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, The Netherlands.
出版信息
BMC Bioinformatics. 2006 Apr 13;7:205. doi: 10.1186/1471-2105-7-205.
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.
背景
DNA微阵列数据模拟至少有三个目的：（i）优化预期的DNA微阵列实验设计；（ii）比较现有的预处理和处理方法，以便对给定的DNA微阵列实验进行最佳分析；（iii）通过让学生、实验室工作人员和其他研究人员了解影响DNA微阵列实验的诸多因素来对他们进行培训。
结果
我们的模型有多层影响实验的因素。这些因素的相对影响在不同实验室、同一实验室的不同实验等之间可能有显著差异。因此，我们添加了一个模块，以便从给定的数据集中粗略估计它们的参数。这保证了我们模拟的数据尽可能接近真实数据。
结论
我们引入了一个用于模拟双染料cDNA微阵列数据的模型，该模型与真实数据非常相似，并将该模型及其软件实现命名为“SIMAGE”，即微阵列基因表达数据模拟。该软件可从以下网址免费获取：http://bioinformatics.biol.rug.nl/websoftware/simage 。
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