pcr: an R package for quality assessment, analysis and testing of qPCR data

PeerJ. 2018 Mar 16;6:e4473. doi: 10.7717/peerj.4473. eCollection 2018.

Abstract

Background: Real-time quantitative PCR (qPCR) is a broadly used technique in the biomedical research. Currently, few different analysis models are used to determine the quality of data and to quantify the mRNA level across the experimental conditions.

Methods: We developed an R package to implement methods for quality assessment, analysis and testing qPCR data for statistical significance. Double Delta CT and standard curve models were implemented to quantify the relative expression of target genes from CT in standard qPCR control-group experiments. In addition, calculation of amplification efficiency and curves from serial dilution qPCR experiments are used to assess the quality of the data. Finally, two-group testing and linear models were used to test for significance of the difference in expression control groups and conditions of interest.

Results: Using two datasets from qPCR experiments, we applied different quality assessment, analysis and statistical testing in the pcr package and compared the results to the original published articles. The final relative expression values from the different models, as well as the intermediary outputs, were checked against the expected results in the original papers and were found to be accurate and reliable.

Conclusion: The pcr package provides an intuitive and unified interface for its main functions to allow biologist to perform all necessary steps of qPCR analysis and produce graphs in a uniform way.

Keywords: Data analysis; Quality assessment; R package; qPCR.

Grant support

This work was supported by the Basic Science Research Program through the National Research Foundation of Korea funded by the Ministry of Education (2015R1D1A01019753) and by the Ministry of Science, ICT and Future Planning (NRF-2015R1A5A2008833). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.