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BMC Genomics. 2009; 10: 153.
Published online Apr 8, 2009. doi:  10.1186/1471-2164-10-153
PMCID: PMC2679054
Learning from microarray interlaboratory studies: measures of precision for gene expression
David L Duewer,corresponding author1 Wendell D Jones,2 Laura H Reid,2 and Marc Salit3
1Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8390, USA
2Expression Analysis, 4324 South Alston Avenue, Suite 101, Durham, North Carolina 27713, USA
3Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8313, USA
corresponding authorCorresponding author.
David L Duewer: david.duewer/at/nist.gov; Wendell D Jones: wjones/at/ExpressionAnalysis.com; Laura H Reid: Lreid2012/at/nc.rr.com; Marc Salit: marc.salit/at/nist.gov
Received July 11, 2008; Accepted April 8, 2009.
Abstract
Background
The ability to demonstrate the reproducibility of gene expression microarray results is a critical consideration for the use of microarray technology in clinical applications. While studies have asserted that microarray data can be "highly reproducible" under given conditions, there is little ability to quantitatively compare amongst the various metrics and terminology used to characterize and express measurement performance. Use of standardized conceptual tools can greatly facilitate communication among the user, developer, and regulator stakeholders of the microarray community. While shaped by less highly multiplexed systems, measurement science (metrology) is devoted to establishing a coherent and internationally recognized vocabulary and quantitative practice for the characterization of measurement processes.
Results
The two independent aspects of the metrological concept of "accuracy" are "trueness" (closeness of a measurement to an accepted reference value) and "precision" (the closeness of measurement results to each other). A carefully designed collaborative study enables estimation of a variety of gene expression measurement precision metrics: repeatability, several flavors of intermediate precision, and reproducibility. The three 2004 Expression Analysis Pilot Proficiency Test collaborative studies, each with 13 to 16 participants, provide triplicate microarray measurements on each of two reference RNA pools. Using and modestly extending the consensus ISO 5725 documentary standard, we evaluate the metrological precision figures of merit for individual microarray signal measurement, building from calculations appropriate to single measurement processes, such as technical replicate expression values for individual probes on a microarray, to the estimation and display of precision functions representing all of the probes in a given platform.
Conclusion
With only modest extensions, the established metrological framework can be fruitfully used to characterize the measurement performance of microarray and other highly multiplexed systems. Precision functions, summarizing routine precision metrics estimated from appropriately repeated measurements of one or more reference materials as functions of signal level, are demonstrated and merit further development for characterizing measurement platforms, monitoring changes in measurement system performance, and comparing performance among laboratories or analysts.
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