Assessing Technical Performance in Differential Gene Expression Experiments with External Spike-in RNA Control Ratio Mixtures
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.
Cite
@article{arxiv.1406.4893,
title = {Assessing Technical Performance in Differential Gene Expression Experiments with External Spike-in RNA Control Ratio Mixtures},
author = {Sarah A. Munro and Steve P. Lund and P. Scott Pine and Hans Binder and Djork-Arné Clevert and Ana Conesa and Joaquin Dopazo and Mario Fasold and Sepp Hochreiter and Huixiao Hong and Nederah Jafari and David P. Kreil and Paweł P. Łabaj and Sheng Li and Yang Liao and Simon Lin and Joseph Meehan and Christopher E. Mason and Javier Santoyo and Robert A. Setterquist and Leming Shi and Wei Shi and Gordon K. Smyth and Nancy Stralis-Pavese and Zhenqiang Su and Weida Tong and Charles Wang and Jian Wang and Joshua Xu and Zhan Ye and Yong Yang and Ying Yu and Marc Salit},
journal= {arXiv preprint arXiv:1406.4893},
year = {2014}
}
Comments
65 pages, 6 Main Figures, 33 Supplementary Figures