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J Immunol Methods. 2017 Nov;450:10-16. doi: 10.1016/j.jim.2017.07.004. Epub 2017 Jul 18.

SLDAssay: A software package and web tool for analyzing limiting dilution assays.

Author information

1
Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA. Electronic address: itrumble@unc.edu.
2
Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA.
3
Division of Infectious Diseases, Center for AIDS Research, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.
4
Quantitative Sciences Unit, Stanford University School of Medicine, Palo Alto, CA 94304, USA.

Abstract

Serial limiting dilution (SLD) assays are used in many areas of infectious disease related research. This paper presents SLDAssay, a free and publicly available R software package and web tool for analyzing data from SLD assays. SLDAssay computes the maximum likelihood estimate (MLE) for the concentration of target cells, with corresponding exact and asymptotic confidence intervals. Exact and asymptotic goodness of fit p-values, and a bias-corrected (BC) MLE are also provided. No other publicly available software currently implements the BC MLE or the exact methods. For validation of SLDAssay, results from Myers et al. (1994) are replicated. Simulations demonstrate the BC MLE is less biased than the MLE. Additionally, simulations demonstrate that exact methods tend to give better confidence interval coverage and goodness-of-fit tests with lower type I error than the asymptotic methods. Additional advantages of using exact methods are also discussed.

KEYWORDS:

Dilution assay; HIV; Infectious units; Latency; Maximum likelihood estimation; Software

PMID:
28733216
PMCID:
PMC5595663
DOI:
10.1016/j.jim.2017.07.004
[Indexed for MEDLINE]
Free PMC Article

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