title: Methods for comparing multiple digital PCR experiments.
abstract: The estimated mean copy per partition (λ) is the essential information from a digital PCR (dPCR) experiment because λ can be used to calculate the target concentration in a sample. However, little information is available how to statistically compare dPCR runs of multiple runs or reduplicates. The comparison of λ values from several runs is a multiple comparison problem, which can be solved using the binary structure of dPCR data. We propose and evaluate two novel methods based on Generalized Linear Models (GLM) and Multiple Ratio Tests (MRT) for comparison of digital PCR experiments. We enriched our MRT framework with computation of simultaneous confidence intervals suitable for comparing multiple dPCR runs. The evaluation of both statistical methods support that MRT is faster and more robust for dPCR experiments performed in large scale. Our theoretical results were confirmed by the analysis of dPCR measurements of dilution series. Both methods were implemented in the dpcR package (v. 0.2) for the open source R statistical computing environment.
authors.affiliation: University of Wroclaw, Faculty of Biotechnology, Department of Genomics, Wroclaw, Poland.
authors.forename: Michał
authors.initials: M
authors.lastname: Burdukiewicz
authors.affiliation: Institute of Biotechnology, Brandenburg University of Technology Cottbus - Senftenberg, Senftenberg, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Rödiger
authors.affiliation: Wrocław University of Technology, Institute of Mathematics and Computer Science, Poland.
authors.forename: Piotr
authors.initials: P
authors.lastname: Sobczyk
authors.affiliation: Dresden University of Technology, Institute of Clinical Chemistry and Laboratory Medicine, Germany.
authors.forename: Mario
authors.initials: M
authors.lastname: Menschikowski
authors.affiliation: Institute of Biotechnology, Brandenburg University of Technology Cottbus - Senftenberg, Senftenberg, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Schierack
authors.affiliation: University of Wroclaw, Faculty of Biotechnology, Department of Genomics, Wroclaw, Poland.
authors.forename: Paweł
authors.initials: P
authors.lastname: Mackiewicz
keywords: Digital PCR; GLM; Generalized Linear Models; Multiple comparison; dPCR