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A proposed metric for assessing the measurement quality of individual microarrays

DOI: 10.1186/1471-2105-7-35

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Abstract:

We hypothesized that an index of the degree of spatiality of gene expression measurements associated with their physical geographic locations on an array could indicate the summary of the physical reliability of the microarray. We introduced a novel way to formulate this index using a statistical analysis tool. Our approach regressed gene expression intensity measurements on a polynomial response surface of the microarray's Cartesian coordinates. We demonstrated this method using a fixed model and presented results from real and simulated datasets.We demonstrated the potential of such a quantitative metric for assessing the reliability of individual arrays. Moreover, we showed that this procedure can be incorporated into laboratory practice as a means to set quality control specifications and as a tool to determine whether an array has sufficient quality to be retained in terms of spatial correlation of gene expression measurements.Gene expression microarrays are a powerful tool used in molecular biology and genetics for understanding gene expression change in biological processes under normal and pathological conditions [1]. Intensity measurements of gene expression are associated with significant variations as a result of the complex and multi-stage processing involved in microarray experiments. Beyond the variability that may be introduced during the fabrication of arrays as a result of print substrate quality and printing pin anomalies, several processing steps – mRNA sample extraction, amplification and labeling, hybridization, and scanning – may introduce substantial variation in measurements [2]. Although several studies have characterized the potential impact of these latter sources of variation on measurements of gene expression [2-4], methods for assessing the physical measurement quality of individual microarrays are not widely available. If technical replicates for a biological case are available, the degree of concordance between technical replicates ca

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