-Per-chip normalization: This step controls for array-wide variations in intensity across multiple samples that form a given dataset. Arrays, as with all fl uorescence based assays, are subject to signal variation for a variety of reasons, including the effi ciency of the labeling and hybridization reactions and possibly other, less well defi ned variables, such as reagent quality and sample handling. To control for this, samples are normalized by fi rst subtracting background and then employing a normalization algorithm to rescale the diff erence in overall intensity to a fi xed intensity level for all samples across multiple arrays.