Batch effects in cytometry data
‘Batch alignment’ and ‘data integration’
– Batch alignment: samples in each batch are handled as part of a larger pre-planned experiments (i.e. same panels, same reagents, same setup, same instrument settings etc), but samples are processed, stained, and/or acquiried on separate days over a period ot time – Data integration: samples are from independent experiments, where the may be significant differences in sample preparation, staining, reagents, instrument settings, etc.
On this page we describe two approaches for batch alignment. While both can be used for data integration, we do not expand on this approach here. If you would like to learn more about how we apply the later approach, drop us a line on the DISCUSSION page.
The goal is to remove technical sources of variation, while preserving biological differences.
Also approaches from single-cell. Some not well suited to cytometry data due to the number of cells etc, but some can be reasonably adapted.
Some methods more controlled (CytoNorm), other less controlled but more adaptable.
Here we provide