Batch correction
During the sample acquisition period, the flow panel was changed to remove one antibody. Batch correction was performed for samples acquired before and after this change to remove potential bias from downstream analysis. Because the primary flow features were expressed as a fraction of the parent population (falling in the 0-to-1 interval) a variance stabilizing transform (logit) was first applied to each data value, prior to re-centering the second panel to have the same mean as the first. After mean-centering, data were transformed back to the original fraction of parent scale by inverse transform. This procedure was applied separately to all 553 flow features annotated in the main text and supplemental data. Notably, this procedure avoids any batch-corrected feature values artificially falling outside of the original 0 to 1 range. Following batch correction, neither UMAP Component 1 nor Component 2 had a statistically significant difference between panels by unpaired Wilcoxon test.