Single-Channel Array Normalization (SCAN)

Briefly, SCAN is a single-sample approach for gene-expression microarrays. This means that the output for a given microarray sample will be the same whether that sample is processed in isolation or jointly with other samples. The probe-sequence content within each microarray is used to correct for binding-affinity biases that can arise during processing and to standardize variances across the probes. Because samples can be processed individually, the user can process extremely large batches of files with a modest computer-memory footprint. Unlike many normalization methods, SCAN can be applied to any Affymetrix microarray for which an annotation package (that has been constructed using the pdInfoBuilder package) exists in Bioconductor. In the paper mentioned above, we demonstrate that SCAN performs as well as or better than several popular normalization methods on simulated and “real-world” data sets.