Assessing quality and normalization of microarrays: case studies using neurological genomic data

Acta Neurologica Scandinavica
A D HersheyT A Glauser

Abstract

Genomic analysis using microarray tools has the potential benefit of enhancing our understanding of neurological diseases. The analysis of these data is complex due to the large amount of data generated. Many tools have been developed to assist with this, but standard methods of analysis of these tools have not been established. This study analyzed the sensitivity and specificity of different analytical methods for gene identification and presents a standardized approach. Affymetrix HG-U133 plus 2.0 microarray datasets from two neurological diseases - chronic migraine and new-onset epilepsy - were used as source data and methods of analysis for normalization of data and identification of gene changes were compared. Housekeeping genes were used to identify non-specific changes and gender related genes were used to identify specific changes. Initial normalization of data revealed that 5-10% of the microarray were potential outliers due to technical errors. Two separate methods of analysis (dChip and Bioconductor) identified the same microarray chips as outliers. For specificity and sensitivity testing, performing a per-gene normalization was found to be inferior to standard preprocessing procedures using robust multichip average ...Continue Reading

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Citations

Jan 10, 2012·Headache·Andrew HersheyScott Powers
Nov 22, 2012·Epilepsia·Hansel M GreinerTracy A Glauser
Oct 27, 2010·Cephalalgia : an International Journal of Headache·Andrew D HersheyScott W Powers

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