Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures.

TitleAssessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures.
Publication TypeJournal Article
Year of Publication2014
AuthorsMunro SA, Lund SP, Pine SP, Binder H, Clevert D-A, Conesa A, Dopazo J, Fasold M, Hochreiter S, Hong H, Jafari N, Kreil DP, Labaj PP, Li S, Liao Y, Lin SM, Meehan J, Mason CE, Santoyo-Lopez J, Setterquist RA, Shi L, Shi W, Smyth GK, Stralis-Pavese N, Su Z, Tong W, Wang C, Wang J, Xu J, Ye Z, Yang Y, Yu Y, Salit M
Journal TitleNature communications
Volume5
Pages5125
Journal Date2014
ISSN2041-1723
KeywordsRNA-seq
AbstractThere 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.
URLhttp://www.nature.com/ncomms/2014/140925/ncomms6125/full/ncomms6125.html
DOI10.1038/ncomms6125
Alternate JournalNat Commun