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Activity Number:
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223
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Type:
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Contributed
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Date/Time:
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Monday, August 3, 2009 : 2:00 PM to 3:50 PM
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Sponsor:
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IMS
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| Abstract - #304823 |
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Title:
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Genotype Calling Accuracy Varies with the Arrays in the Joint Calling Procedure
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Author(s):
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Yalu Wen*+ and Ming Li and Wenjiang Fu
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Companies:
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Michigan State University and Michigan State University and Michigan State University
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Address:
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847A West Fee Hall, East Lansing, MI, 48824,
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Keywords:
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Array quality ; CRLMM ; Joint calling procedure
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Abstract:
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Oligonucleotide SNP arrays have been used in genome-wide association studies. While numerous genotype calling methods have been studied for the Affymetrix SNP arrays, some major issues have not been fully addressed, such as how genotyping accuracy depends on the array quality and the number of arrays in the multi-array genotype calling procedure. In this paper, we examine this issue with the CRLMM using the HapMap data jointly with our study data. We found that the array image (via dChip) may not always reveal poor quality of arrays. The CDF plot and boxplot of the array probe intensity can identify potential poor quality arrays. The genotyping accuracy on the HapMap data varies with the quality and the number of arrays in the joint genotype calling procedure. We conclude that the CRLMM may yield accurate genotype calls when joined with good quality arrays, but not poor quality arrays.
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