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

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

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.

Publication types

  • Validation Study

MeSH terms

  • Bias
  • CD4 Lymphocyte Count / methods*
  • CD4-Positive T-Lymphocytes / immunology*
  • CD4-Positive T-Lymphocytes / virology
  • Computer Simulation
  • Confidence Intervals
  • HIV Infections / blood
  • HIV Infections / diagnosis*
  • HIV Infections / immunology
  • Humans
  • Internet*
  • Likelihood Functions
  • Phenotype
  • Predictive Value of Tests
  • Reproducibility of Results
  • Software*