Chunk #83 — Methods — Genetic control of ancestry effects on expression — Expression residualization for prediction models

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Analysis of gene expression in the postmortem brain of neurotypical Black Americans reveals contributions of genetic ancestry.

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To generate residualized expression for our prediction models, we fitted a linear model with lmFit from limma to normalize expression (see ‘eQTL analysis’) and covariates (see ‘Global ancestry-associated differential expression analysis’; equation (3)). Using this model, we regressed out covariates from normalized expression using the residuals function in R (v.4.0.3).