wavy patterns in signal intensities of Affymetrix arrays, and they reduce the signal noise by incorporating probe and target sequence characteristics in the Genomic Imbalance Map (GIM) algorithm. Nannya et al. (7) has also described similar phenomenon in CNV studies on cancer genome by the Affymetrix SNP arrays, and this effect was adjusted by the length and GC content of the PCR products using quadratic regressions, for the purpose of compensation for different PCR conditions.
