Abstract—Microarray technology is widely used to determine single nucleotide polymorphism (SNP) genotype calls when studying the association between disease and human subjects. A genotype call is decided relatively with the signal intensity values of spots on the microarray image. Since high-throughput microarray technology can contain millions of SNP spots, it is impossible to manually inspect if the spots are aligned correctly and intensity values are calculated accurately. However, a wrong genotype call will skew the outputted numerical results, which can ultimately cause unsuitable medicine to be prescribed and jeopardize a person’s life. Therefore, retrieving correct intensity values is very important. This paper analyzes and shows the effect signals have on the SNP genotype calls when the signals from the same spots are retrieved and represented in different values.
Index Terms—Genotype, image processing, microarray, SNP.
Ching-Yu Huang is with the Department of Computer Science, Kean University, USA (e-mail: chuang@kean.edu).
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Cite:Ching-Yu Huang, "The Impact of Microarray Image Intensity Variations on SNP Genotype Calls," International Journal of Information and Electronics Engineering vol. 6, no. 3, pp. 198-201, 2016.
