Nucleic Acids Research Advance Access published online on August 1, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn430
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Methods Online |
Consolidated strategy for the analysis of microarray spike-in data
Department of Biostatistics, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, MD 21205, USA
*To whom correspondence should be addressed. Tel: +1 410 614 5157; Fax: +1 410 955 0958; Email: ririzarr{at}jhsph.edu
Received April 17, 2008. Revised June 19, 2008. Accepted June 20, 2008.
As the number of users of microarray technology continues to grow, so does the importance of platform assessments and comparisons. Spike-in experiments have been successfully used for internal technology assessments by microarray manufacturers and for comparisons of competing data analysis approaches. The microarray literature is saturated with statistical assessments based on spike-in experiment data. Unfortunately, the statistical assessments vary widely and are applicable only in specific cases. This has introduced confusion into the debate over best practices with regards to which platform, protocols and data analysis tools are best. Furthermore, cross-platform comparisons have proven difficult because reported concentrations are not comparable. In this article, we introduce two new spike-in experiments, present a novel statistical solution that enables cross-platform comparisons, and propose a comprehensive procedure for assessments based on spike-in experiments. The ideas are implemented in a user friendly Bioconductor package: spkTools. We demonstrated the utility of our tools by presenting the first spike-in-based comparison of the three major platforms–Affymetrix, Agilent and Illumina.