title: A benchmark for microRNA quantification algorithms using the OpenArray platform.
abstract: BACKGROUND
  Several techniques have been tailored to the quantification of microRNA expression, including hybridization arrays, quantitative PCR (qPCR), and high-throughput sequencing. Each of these has certain strengths and limitations depending both on the technology itself and the algorithm used to convert raw data into expression estimates. Reliable quantification of microRNA expression is challenging in part due to the relatively low abundance and short length of the miRNAs. While substantial research has been devoted to the development of methods to quantify mRNA expression, relatively little effort has been spent on microRNA expression.
  
  
  RESULTS
  In this work, we focus on the Life Technologies TaqMan OpenArray(Ⓡ) system, a qPCR-based platform to measure microRNA expression. Several algorithms currently exist to estimate expression from the raw amplification data produced by qPCR-based technologies. To assess and compare the performance of these methods, we performed a set of dilution/mixture experiments to create a benchmark data set. We also developed a suite of statistical assessments that evaluate many different aspects of performance: accuracy, precision, titration response, number of complete features, limit of detection, and data quality. The benchmark data and software are freely available via two R/Bioconductor packages, miRcomp and miRcompData. Finally, we demonstrate use of our software by comparing two widely used algorithms and providing assessments for four other algorithms.
  
  
  CONCLUSIONS
  Benchmark data sets and software are crucial tools for the assessment and comparison of competing algorithms. We believe that the miRcomp and miRcompData packages will facilitate the development of new methodology for microRNA expression estimation.
authors.affiliation: Department of Biostatistics and Computational Biology, University of Rochester, 265 Crittenden Blvd, Rochester, 14642, NY, USA. mccallm@gmail.com.
authors.forename: Matthew N
authors.initials: MN
authors.lastname: McCall
authors.affiliation: Department of Pathology, The Johns Hopkins University, 720 Rutland Ave, Baltimore, 21205, MD, USA.
authors.forename: Alexander S
authors.initials: AS
authors.lastname: Baras
authors.affiliation: Biology Department, The Johns Hopkins University, 3400 N Charles St, Baltimore, 21218, MD, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Crits-Christoph
authors.affiliation: Genetic Resources Core Facility, The Johns Hopkins University, 600 N Wolfe St, Baltimore, 21287, MD, USA.
authors.forename: Roxann
authors.initials: R
authors.lastname: Ingersoll
authors.affiliation: Department of Molecular and Comparative Pathobiology, The Johns Hopkins University, 733 N Broadway, Baltimore, 21205, MD, USA.
authors.forename: Melissa A
authors.initials: MA
authors.lastname: McAlexander
authors.affiliation: Department of Molecular and Comparative Pathobiology, The Johns Hopkins University, 733 N Broadway, Baltimore, 21205, MD, USA.|Department of Neurology, The Johns Hopkins University, 855 N Wolfe St, Baltimore, 21205, MD, USA.
authors.forename: Kenneth W
authors.initials: KW
authors.lastname: Witwer
authors.affiliation: Department of Pathology, The Johns Hopkins University, 720 Rutland Ave, Baltimore, 21205, MD, USA.
authors.forename: Marc K
authors.initials: MK
authors.lastname: Halushka
mesh_terms: D000465:Algorithms; D019985:Benchmarking; D006801:Humans; D057230:Limit of Detection; D035683:MicroRNAs / Q000032:analysis* / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D012984:Software
chemical_list: D035683:MicroRNAs
keywords: Expression; microRNA; qPCR