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Genomics. 2010 Mar;95(3):138-42. doi: 10.1016/j.ygeno.2010.01.003. Epub 2010 Jan 14.

Microarray data quality control improves the detection of differentially expressed genes.

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  • 1EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK. audrey@ebi.ac.uk <audrey@ebi.ac.uk>


Microarrays have become a routine tool for biomedical research. Data quality assessment is an essential part of the analysis, but it is still not easy to perform objectively or in an automated manner, and as a result it is often neglected. Here, we compared two strategies of array-level quality control using five publicly available microarray experiments: outlier removal and array weights. We also compared them against no outlier removal and random array removal. We find that removing outlier arrays can improve the signal-to-noise ratio and thus strengthen the power of detecting differentially expressed genes. Using array weights is similarly effective, but its applicability is more limited. The quality metrics presented here are implemented in the Bioconductor package arrayQualityMetrics.

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