Supplementary materials: Molecular analysis of positional identity in the developing mouse retina

The raw data from a cDNA microarray experiment consist of pairs of image files. Pre-processsing steps such as image anlysis and normalization are required to extract reliable measures of the fluorescence intensities and allowed comparisons within and between slides. All images were processed by Spot with foreground seeds set to 5 pixels square. In addition, within and between slide normalization was performed on all data. For within slide normalization, we used the ”print-tip group scale normalization” method followed by multiple-slide scale normalization allowing comparison of different experiments. Further details of our normalization methods can be found in Yang et al. (2002).