Signal quality measurements for cDNA microarray data

Concerns about the reliability of expression data from microarrays inspire ongoing research into measurement error in these experiments. Error arises at both the technical level within the laboratory and the experimental level. In this paper, we will focus on estimating the spot-specific error, as there are few currently available models. This paper outlines two different approaches to quantify the reliability of spot-specific intensity estimates. In both cases, the spatial correlation between pixels and its impact on spot quality is accounted for. The first method is a straightforward parametric estimate of within-spot variance that assumes a Gaussian distribution and accounts for spatial correlation via an overdispersion factor. The second method employs a nonparametric quality estimate referred to throughout as the mean square prediction error (MSPE). The MSPE first smoothes a pixel region and then measures the difference between actual pixel values and the smoother. Both methods herein are compared for real and simulated data to assess numerical characteristics and the ability to describe poor spot quality. We conclude that both approaches capture noise in the microarray platform and highlight situations where one method or the other is superior.