Mass cytometry (CyTOF) is a technology that has revolutionised single cell biology. By detecting over 40 proteins on millions of single cells, CyTOF allows the characterisation of cell subpopulations in unprecedented detail. However most CyTOF studies require the integration of data from multiple CyTOF batches usually acquired on different days and possibly at different sites. To date, the integration of CyTOF datasets remains a challenge due to technical differences arising in multiple batches. To overcome this limitation, we developed an approach called CytofRUV for analysing multiple CyTOF batches which includes an R-Shiny application with diagnostics plots. CytofRUV can correct for batch effects and integrate data from large numbers of patients and conditions across batches, to confidently compare cellular changes and correlate these with clinically relevant outcomes.
- Marie Trussart
- Terence P Speed
- Daniel HD Gray
- Daniel HD Gray
- Charis E Teh
- Tania Tan
- Charis E Teh
- Lawrence Leong
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Human subjects: All patients provided written informed consent and the study was approved by Human Research Ethics Committees/Institutional Review Boards: RMH (2005.008, 2012.244, 2016.305,2016.066) and the Walter and Eliza Hall Institute (G15/05).
- Greg Finak
- Received: June 3, 2020
- Accepted: September 5, 2020
- Accepted Manuscript published: September 7, 2020 (version 1)
© 2020, Trussart et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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