Protein multiplexed immunoassay analysis with R

Edmond J. Breen*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

6 Citations (Scopus)


Plasma samples from 177 control and type 2 diabetes patients collected at three Australian hospitals are screened for 14 analytes using six custom-made multiplex kits across 60 96-well plates. In total 354 samples were collected from the patients, representing one baseline and one end point sample from each patient. R methods and source code for analyzing the analyte fluorescence response obtained from these samples by Luminex Bio-Plex® xMap multiplexed immunoassay technology are disclosed. Techniques and R procedures for reading Bio-Plex® result files for statistical analysis and data visualization are also presented. The need for technical replicates and the number of technical replicates are addressed as well as plate layout design strategies. Multinomial regression is used to determine plate to sample covariate balance. Methods for matching clinical covariate information to Bio-Plex® results and vice versa are given. As well as methods for measuring and inspecting the quality of the fluorescence responses are presented. Both fixed and mixed-effect approaches for immunoassay statistical differential analysis are presented and discussed. A random effect approach to outlier analysis and detection is also shown. The bioinformatics R methodology present here provides a foundation for rigorous and reproducible analysis of the fluorescence response obtained from multiplexed immunoassays.

Original languageEnglish
Title of host publicationSerum/plasma proteomics
Subtitle of host publicationmethods and protocols
EditorsDavid W. Greening, Richard J. Simpson
Place of PublicationNew York
PublisherHumana Press Inc.
Number of pages43
ISBN (Electronic)9781493970575
ISBN (Print)9781493970568
Publication statusPublished - 2017

Publication series

NameMethods in molecular biology
PublisherHumana Press
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Multiplex immunoassay analysis
  • R programming language
  • Mixed-effects model
  • Proteomics
  • xMap
  • Quality
  • Bioinformatics


Dive into the research topics of 'Protein multiplexed immunoassay analysis with R'. Together they form a unique fingerprint.

Cite this