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There is a critical need for standard approaches to assess, report, andcompare the technical performance of genome-scale differential gene expressionexperiments. We assess technical performance with a proposed "standard"dashboard of metrics derived from analysis of external spike-in RNA controlratio mixtures. These control ratio mixtures with defined abundance ratiosenable assessment of diagnostic performance of differentially expressedtranscript lists, limit of detection of ratio (LODR) estimates, and expressionratio variability and measurement bias. The performance metrics suite isapplicable to analysis of a typical experiment, and here we also apply thesemetrics to evaluate technical performance among laboratories. Aninterlaboratory study using identical samples shared amongst 12 laboratorieswith three different measurement processes demonstrated generally consistentdiagnostic power across 11 laboratories. Ratio measurement variability and biaswere also comparable amongst laboratories for the same measurement process.Different biases were observed for measurement processes using different mRNAenrichment protocols.

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