Yunhao Jiang

Cell proportions from bulk RNA sequencing are inferred through a single-cell reference, and that reference can change the conclusion drawn from them. In 981 PBMC donors the CD8 T-cell age association reversed in all 80 six-type references and the CD4 slope was inflated about 6.3-fold; in 48 islet donors a borderline alpha-cell association became significant in 54% to 100% of references. The error recurred across four estimator classes, its direction was set by the estimator, and fit accuracy did not flag it.

Cell proportions from bulk RNA sequencing are inferred through a single-cell reference, and that reference can change the conclusion drawn from them. In 981 PBMC donors the CD8 T-cell age association reversed in all 80 six-type references and the CD4 slope was inflated about 6.3-fold; in 48 islet donors a borderline alpha-cell association became significant in 54% to 100% of references. The error recurred across four estimator classes, its direction was set by the estimator, and fit accuracy did not flag it.