Extending Microarray Quality Control and Analysis Algorithms to Illumina Chip Platform

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Abstract
This paper presents a novel data quality control technique for a challenging new microarray platform supplied by Illumina, Inc. Microarray is a revolutionary biotechnology that enables the study of thousands of genes and proteins simultaneously. While the type of microarray chip platforms keeps increasing and the manufacture quality keeps improving, the array data quality control and analysis tools are still lagging behind. In this research, we design an adaptable microarray data quality control and analysis system capable of handling multiple microarray platforms. We demonstrate that the Illumina chips, even though the layouts are randomly assembled, still contain artifacts. We conclude that it is necessary for chip manufacturers to provide low-level bead location output as a standard feature for better data quality assurance.