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Removing unwanted variation with CytofRUV to integrate multiple CyTOF datasets.

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 diagnostic 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.

SUBMITTER: Trussart M

PROVIDER: S-EPMC7500954 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Removing unwanted variation with CytofRUV to integrate multiple CyTOF datasets.

Trussart Marie M Teh Charis E CE Tan Tania T Leong Lawrence L Gray Daniel Hd DH Speed Terence P TP

eLife 20200907

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 ...[more]

PMID: 32894218

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