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arXiv · 1406.4893

Assessing Technical Performance in Differential Gene Expression Experiments with External Spike-in RNA Control Ratio Mixtures

Sarah A. Munro·Steve P. Lund·P. Scott Pine·Hans Binder·Djork-Arné Clevert·Ana Conesa·Joaquin Dopazo·Mario Fasold·Sepp Hochreiter·Huixiao Hong·Nederah Jafari·David P. Kreil·Paweł P. Łabaj·Sheng Li·Yang Liao·Simon Lin·Joseph Meehan·Christopher E. Mason·Javier Santoyo·Robert A. Setterquist·Leming Shi·Wei Shi·Gordon K. Smyth·Nancy Stralis-Pavese·Zhenqiang Su·Weida Tong·Charles Wang·Jian Wang·Joshua Xu·Zhan Ye·Yong Yang·Ying Yu·Marc Salit
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Abstract

There is a critical need for standard approaches to assess, report, and compare the technical performance of genome-scale differential gene expression experiments. We assess technical performance with a proposed "standard" dashboard of metrics derived from analysis of external spike-in RNA control ratio mixtures. These control ratio mixtures with defined abundance ratios enable assessment of diagnostic performance of differentially expressed transcript lists, limit of detection of ratio (LODR) estimates, and expression ratio variability and measurement bias. The performance metrics suite is applicable to analysis of a typical experiment, and here we also apply these metrics to evaluate technical performance among laboratories. An interlaboratory study using identical samples shared amongst 12 laboratories with three different measurement processes demonstrated generally consistent diagnostic power across 11 laboratories. Ratio measurement variability and bias were also comparable amongst laboratories for the same measurement process. Different biases were observed for measurement processes using different mRNA enrichment protocols.

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Sarah A. Munro, Steve P. Lund, P. Scott Pine, Hans Binder, Djork-Arné Clevert, Ana Conesa, Joaquin Dopazo, Mario Fasold, Sepp Hochreiter, Huixiao Hong, Nederah Jafari, David P. Kreil, Paweł P. Łabaj, Sheng Li, Yang Liao, Simon Lin, Joseph Meehan, Christopher E. Mason, Javier Santoyo, Robert A. Setterquist, Leming Shi, Wei Shi, Gordon K. Smyth, Nancy Stralis-Pavese, Zhenqiang Su, Weida Tong, Charles Wang, Jian Wang, Joshua Xu, Zhan Ye, Yong Yang, Ying Yu, Marc Salit. 2014-06-18. Assessing Technical Performance in Differential Gene Expression Experiments with External Spike-in RNA Control Ratio Mixtures. https://doi.org/10.1038/ncomms6125

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