Removing unwanted variation with CytofRUV to integrate multiple CyTOF datasets

Abstract
Data availability
Article and author information
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Abstract

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.

Data availability

Flow Repository: The fcs files from this study are available at flow repository ID FR-FCM-Z2L2.

The following data sets were generated

1. Trussart M
2. Teh CE
3. Tan T
4. Leong L
5. Gray DHD
6. Speed TP
(2020) CytofRUV dataset
Flowrepository.org database, FR-FCM-Z2L2.

http://flowrepository.org/id/RvFrVB2mAm2q08TjrWBEaJ4scGfMTPDwZiToOS22zcMztKarmVH563xYyFW78ZAL

The following previously published data sets were used

1. Sofie Van Gassen
(2019) Immune Clock of Pregnancy Validation - Controls
Flowrepository.org database, FR-FCM-Z247.

http://flowrepository.org/id/FR-FCM-Z247

Article and author information

Author details

Marie Trussart

Bioinformatics, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia

For correspondence
trussart.m@wehi.edu.au

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-7258-7272
Charis E Teh

Bioinformatics, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia

Competing interests
The authors declare that no competing interests exist.
Tania Tan

Bioinformatics, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia

Competing interests
The authors declare that no competing interests exist.
Lawrence Leong

Bioinformatics, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia

Competing interests
The authors declare that no competing interests exist.
Daniel HD Gray

Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-8457-8242
Terence P Speed

Bioinformatics, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia

Competing interests
The authors declare that no competing interests exist.

Funding

National Health and Medical Research Council (1054618)

Marie Trussart
Terence P Speed

National Health and Medical Research Council (1158024)

Daniel HD Gray

Cancer Council Victoria (1146518)

Daniel HD Gray

National Health and Medical Research Council (1089072)

Charis E Teh

Cancer Council Victoria (1146518)

Tania Tan

Perpetual Impact Philanthropy (IPAP2019/1437)

Charis E Teh

UROP Fellowship

Lawrence Leong

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

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).

Copyright

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.