Open Access Highly Accessed Methodology article

Assessing affymetrix GeneChip microarray quality

Matthew N McCall1, Peter N Murakami2, Margus Lukk34, Wolfgang Huber5 and Rafael A Irizarry6*

Author Affiliations

1 Department of Biostatistics and Computational Biology, University of Rochester Medical Center, 601 Elmwood Ave., Rochester, NY, USA

2 Center for Epigenetics, Johns Hopkins School of Medicine, 855 N. Wolfe St., Baltimore, MD, USA

3 EMBL-EBI Functional Genomics Group, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

4 Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 ORE, UK

5 EMBL Genome Biology Unit, 69117 Heidelberg, Germany

6 Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St., Baltimore, MD, USA

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BMC Bioinformatics 2011, 12:137  doi:10.1186/1471-2105-12-137

Published: 7 May 2011

Additional files

Additional file 1:

Supplementary Figures. Figures S1-S7.

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Additional file 2:

GNUSE by Study. Table containing the overall quality of the 809 MIAME-compliant microarray studies available via GEO in December 2009. For each study, we report the number of arrays, the average GNUSE median, and the proportion of poor quality arrays (GNUSE median > 1.25).

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