Conference Paper

On Single-Array Genotype Calling Algorithms

Dept. of Med., Univ. of Chicago, Chicago, IL
DOI: 10.1109/BMEI.2008.107 Conference: BioMedical Engineering and Informatics, 2008. BMEI 2008. International Conference on, Volume: 1
Source: IEEE Xplore

ABSTRACT This paper describes issues in using single-array algorithms for calling genotypes for Affymetrix arrays, and introduces a computationally efficient procedure that is designed to be used as a complement to the multi-arrays algorithms. The new tool is based on ideas from a previously introduced algorithm [9] with modifications that improve accuracy. These modifications are also necessary for handling the data from the new arrays which have a modified design with no perfect-matches. The main gain in accuracy is obtained from the partitioning of the probes in homogeneous clusters based on measures of efficiency of probe hybridization that are calculated from the probe sequence composition, and based on measures of probe performance that are calculated using a small training dataset.

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