Journal article
Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures
SA Munro, SP Lund, PS Pine, H Binder, DA Clevert, A Conesa, J Dopazo, M Fasold, S Hochreiter, H Hong, N Jafari, DP Kreil, PP Łabaj, S Li, Y Liao, SM Lin, J Meehan, CE Mason, J Santoyo-Lopez, RA Setterquist Show all
Nature Communications | Published : 2014
DOI: 10.1038/ncomms6125
Abstract
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 te..
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Awarded by Biotechnology and Biological Sciences Research Council
Funding Acknowledgements
We thank David L. Duewer and Jerod Parsons for review of the manuscript, Cecelie Boysen for discussion of results and all other members of the SEQC consortium who supported this work. P.P.L., N.S.-P. and D.P.K. acknowledge the support from the Vienna Scientific Cluster (VSC),the Vienna Science and Technology Fund (WWTF), Baxter AG, Austrian Research Centres (ARC) Seibersdorf and the Austrian Centre of Biopharmaceutical Technology (ACBT). J.D. was supported by grant BIO2011-27069 from the Spanish Ministry of Economy and Competitiveness (MINECO). L.S. and Y.Yu acknowledge support from China's National Supercomputing Center in Guangzhou.