2.1. DNA Microarray Data Simulators
There are several DNA microarray data simulators. Albers et al., suggest SIMAGE, a model and web based software implementation for simulating dual-dye DNA microarray data [8]. Their proposed model requires the specification of up to 29 parameters including biological and technical parameters. They discuss that model parameters are strongly dependent on the experiment performed, and they may even vary in different experiments performed in the same laboratory. SIMAGE is designed for simulating dual-dye DNA microarray data and cannot be used for generating single channel microarray data. The authors state that due to specific properties of each type of DNA microarray, creating data simulators for other microarray platforms would be a useful and interesting direction for future research.
Dembélé proposed a model to simulate log2 intensity data or log2 ratio data for DNA microarrays [9]. As pointed out earlier, this is problematic for generating artificial kinome data where background-corrected values can be negative. In addition, model was constructed based on the assumption that intensities for each gene are uniformly distributed around its average. The noise component in the model is also normally distributed with a zero mean and a standard deviation, which is a parameter for the model. Therefore, generated microarray data from this method have a constant variance, which is not a realistic assumption for kinome microarray data, which suffer from heterogeneous variance; i.e., there is a relation between mean and variance.
Nykter et al. [10] utilized several available error models to formulate biological and measurement variation in order to simulate microarray data with realistic characteristics. To represent the steps that may affect the quality of microarray data, they used noise, slide, hybridization, scanner, and error models. The models are controlled by multiple parameters, for a total of 94. It is not clear what parameter values should be used for generating kinome array data, or how such values would be determined. If nothing else, the task of determining values for such a large number of parameters discourages the method’s use.