In the context of cytometry, batch effects refers to channel intensity changes due to technical variation that has no biological implication. A common example is acquiring samples over a long time period. Changes in reagents, operators, pipetting, etc. all influence channel intensities.
Astrolabe never compares numerical intensities between samples. Each sample is analyzed separately, and then comparisons are done using either cell frequencies (such as comparing T Cell counts) or qualitative values (“CD3 high” versus “CD3 low”). The underlying assumption is that a given subset is the same whether the underlying marker intensity is shifted or not&emdash;in other words, a T Cell is a T Cell whether the CD3+ peak is centered around a transformed intensity of 4, or a transformed intensity of 6. This mirrors the approach utilized in manual analysis.
Since intensities are never directly compared, the platform is highly resilient to batch effects.