Why do I need to purchase an additional Affymetrix array set for Input DNA?
Affymetrix arrays are tiled with 25-mer probes across the genome (except for repetitive sequences). These probes exhibit different hybridization kinetics due to varying GC-content and sequence composition. Therefore, hybridization with Input DNA is necessary to normalize for differences in hybridization efficiencies of the probes. Additionally, the control array normalizes for copy number variations that could otherwise result in false positives. Affymetrix tiling arrays (tiled at very high density) were developed such that the control hybridizations for each array type are carried out on a separate array. Thus, one additional set of Input DNA arrays when using the 7-array full genome set (or one array if using only one array type or the promoter array) is required in each assay.
