Visual Quality Control With CytoMDS a Bioconductor Package for Low Dimensional Representation of Cytometry Sample Distances
(2025) Cytometry. Part A — Vol. 107, n° 3, p. 177-186 (2025)
Files
Visual Quality Control With CytoMDS , a Bioconductor Package for Low Dimensional Representation of Cytometry Sample Distances.pdf
Open Access - Adobe PDF
- 12.78 MB
Details
- Authors
Hauchamps, Philippe 
Delandre, Simon Temmerman, Stéphane T.
- Abstract
- <jats:title>ABSTRACT</jats:title> <jats:p> Quality Control (QC) of samples is an essential preliminary step in cytometry data analysis. Notably, the identification of potential batch effects and outlying samples is paramount to avoid mistaking these effects for true biological signals in downstream analyses. However, this task can prove to be delicate and tedious, especially for datasets with dozens of samples. Here, we present <jats:italic>CytoMDS</jats:italic> , a Bioconductor package implementing a dedicated method for low‐dimensional representation of cytometry samples composed of marker expressions for up to millions of single cells. This method allows a global representation of all samples of a study, with one single point per sample, in such a way that projected distances can be visually interpreted. <jats:italic>CytoMDS</jats:italic> uses <jats:italic>Earth Mover's Distance</jats:italic> for assessing dissimilarities between multi‐dimensional distributions of marker expression and <jats:italic>Multi‐Dimensional Scaling</jats:italic> for low‐dimensional projection of distances. Some additional visualization tools, both for projection quality diagnosis and for user interpretation of the projection coordinates, are also provided in the package. We demonstrate the strengths and advantages of <jats:italic>CytoMDS</jats:italic> for QC of cytometry data on three real biological datasets, revealing the presence of low‐quality samples, batch effects, and biological signal between sample groups. </jats:p>
- Affiliations
Citations
Hauchamps, P., Delandre, S., Temmerman, S. T., Lin, D., & Gatto, L. (2025). Visual Quality Control With CytoMDS a Bioconductor Package for Low Dimensional Representation of Cytometry Sample Distances. Cytometry. Part A, 107(3), 177-186. https://doi.org/10.1002/cyto.a.24921 (Original work published 2025)