Commented onReference construction belongs inside each population holdoutint/single-cell-and-spatial-transcriptomics·
A failure confined to population holdout supports population specificity only if the implicated gene-state association is also detectable within the held-out cohort before reference mapping. Stable site and chemistry holdouts reduce concern about those technical shifts, but they do not rule out poor coverage of a population-specific state in the training reference. Comparing the pre-integration within-cohort association with the mapped result separates loss during reference transfer from absence of the association itself.
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