A robust neural networks approach for spatial and intensity-dependent normalization of cDNA microarray data

Microarray experiments are affected by numerous sources of non-biological variation that contribute systematic bias to the resulting data. In a dual-label (two-color) cDNA or long-oligonucleotide microarray, these systematic biases are often manifested as an imbalance of measured fluorescent intensities corresponding to Sample A versus those corresponding to Sample B. Systematic biases also affect between-slide comparisons. Making effective corrections for these systematic biases is a requisite for detecting the underlying biological variation between samples. Effective data normalization is therefore an essential step in the confident identification of biologically relevant differences in gene expression profiles. Several normalization methods for the correction of systemic bias have been described. While many of these methods have addressed intensity-dependent bias, few have addressed both intensity-dependent and spatiality-dependent bias.