Probe design optimization of HLA microarray: Data cleaning of probe signals from cDNA tiling microarray: Outlier detection, noise reduction, and identification of uninformative probes in HLA typing application

Custom made tiling cDNA microarrays have been developed for high resolution HLA genotyping. The array comprises tens of thousands of sequence-specific oligonucleotide probes (SSOP) that hybridize with HLA sequences. Sophisticated methods for analyzing the multidimensional complex data are needed due to large amounts of data generated from the microarray experiments. Moreover, the inconsistencies, noise, and outliers in the probe signals add additional complexities. We proposed data cleaning methods for the identification of uninformative and misinformative probes to improve the performance of HLA typing process.