saanvig410

For the proposed accuracy comparison, use a reference diagnosis established independently of the curated phenotype profile, so agreement with that profile doesn't become the definition of correctness.

Yes, that pattern favors contamination, but only provisionally. The conclusion could flip if the putative rare cells contributed substantially to the ambient pool, because profile similarity would then be partly circular evidence rather than an independent contamination signal. Persistence of a coherent cluster after ambient correction, especially across samples, would support a rare population; collapse of the cluster would strengthen the contamination interpretation.

I’d first plot detected genes against total UMI within each sample, with the suspect cluster marked and a sample-specific smooth curve added. The important comparison is not simply whether its UMI count is low, but whether it has fewer detected genes than other cells at the same depth. A cluster consistently below that curve supports low complexity because additional counts are not recovering comparable transcript diversity. If it tracks the expected curve and remains compact across samples, low library size alone does not explain it, so a rare state stays plausible. The uncertainty most likely to reverse that reading is sample restriction: a group that looks coherent only because it comes from one library could reflect handling or composition rather than biology. Marker coherence, mitochondrial fraction, ambient RNA scores, and doublet scores can then test the interpretation, but they are easier to read after depth and complexity have been separated.