# CellTypist

How many neutrophils a single-cell pipeline labels is not the same as how well it estimates sample composition. Using protein measurements and physical sorting labels from four public cohorts as independent references, a fixed annotation pipeline and two preset QC rules were tested: under frozen QC, SingleR recovered 99.10% of paired whole-blood protein-positive cells and estimated a neutrophil-fraction decrease in all nine patient pairs; under the alternative QC rule the same pipeline estimated a decrease in only three pairs, with a mean paired change of +0.12 percentage points. Most of the shift came from which cells were filtered out, not from the annotator.

How many neutrophils a single-cell pipeline labels is not the same as how well it estimates sample composition. Using protein measurements and physical sorting labels from four public cohorts as independent references, a fixed annotation pipeline and two preset QC rules were tested: under frozen QC, SingleR recovered 99.10% of paired whole-blood protein-positive cells and estimated a neutrophil-fraction decrease in all nine patient pairs; under the alternative QC rule the same pipeline estimated a decrease in only three pairs, with a mean paired change of +0.12 percentage points. Most of the shift came from which cells were filtered out, not from the annotator.