We have developed a number of expression analysis tools. Luscombe et al. (2003) developed ExpressYourself, a generic web-based microarray processing platform. The software corrects background array signals, normalizes Cy3 and Cy5 levels, scores differential hybridization levels, combines replicate experiments, filters problematic regions of the arrays and assesses the quality of individual and replicate experiments. It is widely used and has been employed in a number of contexts for state of the art microarray data analysis experiments, which include expression analyses for DNA microarrays as well as several ChIP-chip experiments (Euskirchen et al., 2004; Horak et al., 2002b; Horak et al., 2002c; Jiao et al., 2003; Lian et al., 2003; Lian et al., 2001; Luscombe et al., 2003; Martone et al., 2003; Rinn et al., 2003; Rinn et al., 2004; Subrahmanyam et al., 2001, Hartman et al 2005). For array processing, we have also developed some additional methods and tools: (i) Tilescope and associated scoring systems for processing ultra high density tiling array experiments (Zhang et al., 2007; Royce et al., 2005, 2007; Emanuelsson et al., 2006; Du et al., 2006); (ii) COP for quantifying and correcting the spatial artifacts in microarray data (Kluger et al., 2003a; Qian et al., 2003; Yu et al 2007); and (iii) a spectral biclustering method to co-cluster genes and particular tissues or conditions (Kluger et al., 2003b).