TY - JOUR T1 - Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures. JF - Nature communications Y1 - 2014 A1 - Munro, Sarah A A1 - Lund, Steven P A1 - Pine, P Scott A1 - Binder, Hans A1 - Clevert, Djork-Arné A1 - Ana Conesa A1 - Dopazo, Joaquin A1 - Fasold, Mario A1 - Hochreiter, Sepp A1 - Hong, Huixiao A1 - Jafari, Nadereh A1 - Kreil, David P A1 - Labaj, Paweł P A1 - Li, Sheng A1 - Liao, Yang A1 - Lin, Simon M A1 - Meehan, Joseph A1 - Mason, Christopher E A1 - Santoyo-López, Javier A1 - Setterquist, Robert A A1 - Shi, Leming A1 - Shi, Wei A1 - Smyth, Gordon K A1 - Stralis-Pavese, Nancy A1 - Su, Zhenqiang A1 - Tong, Weida A1 - Wang, Charles A1 - Wang, Jian A1 - Xu, Joshua A1 - Ye, Zhan A1 - Yang, Yong A1 - Yu, Ying A1 - Salit, Marc KW - RNA-seq AB - There is a critical need for standard approaches to assess, report and compare the technical performance of genome-scale differential gene expression experiments. Here 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 among 12 laboratories with three different measurement processes demonstrates generally consistent diagnostic power across 11 laboratories. Ratio measurement variability and bias are also comparable among laboratories for the same measurement process. We observe different biases for measurement processes using different mRNA-enrichment protocols. VL - 5 UR - http://www.nature.com/ncomms/2014/140925/ncomms6125/full/ncomms6125.html ER -