Researchers have used techniques from the area of transcriptional DNA microarrays to solve problems in the kinome microarray context. Since the chemistry involved in kinome microarray technologies differs from that of DNA microarrays, data analysis techniques appropriate for DNA microarrays may not be appropriate for kinome microarrays [5]. In addition, some characteristics of kinome arrays such as number of spots on an array and number of within-array replicates differ from those of DNA microarrays. These characteristics may affect downstream data analyses techniques. Therefore evaluating various algorithms and methodologies used by the DNA microarray community before applying them in kinome array data analysis is essential.