Data analysis was performed using the workflow previously developed (23 (link)). Briefly, after acquisition, intrafile signal drift was normalized and.fcs files were obtained using CyTOF software. To diminish batch effects, all files were normalized on EQ Beads (Fluidigm) using the premessa R package (https://github.com/ParkerICI/premessa). Raw median intensity values were transformed to a hyperbolic arcsine (arcsinh) and then analysis was performed using Cytobank software (Beckman Coulter, Brea, CA, USA).
Le Gallou S., Lhomme F., Irish J.M., Mingam A., Pangault C., Monvoisin C., Ferrant J., Azzaoui I., Rossille D., Bouabdallah K., Damaj G., Cartron G., Godmer P., Le Gouill S., Casasnovas R.O., Molina T.J., Houot R., Lamy T., Tarte K., Fest T, & Roussel M. (2021). Nonclassical Monocytes Are Prone to Migrate Into Tumor in Diffuse Large B-Cell Lymphoma. Frontiers in Immunology, 12, 755623.
Other organizations :
Université de Rennes, Inserm, Centre Hospitalier Universitaire de Rennes, Vanderbilt University, Centre Hospitalier Universitaire de Bordeaux, Centre Hospitalier Universitaire de Caen, Université de Caen Normandie, Centre hospitalier Bretagne Atlantique, Centre Hospitalier Universitaire de Nantes, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, Centre Hospitalier Universitaire Dijon Bourgogne, Hôpital Necker-Enfants Malades, Assistance Publique – Hôpitaux de Paris
EQ Beads (Fluidigm) used for normalization to diminish batch effects
controls
Positive control: EQ Beads (Fluidigm) used for normalization
Negative control: Not explicitly mentioned
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