Otherwise, to generate input for the eQTL and network analyses, we directly used the lm() function in R, and the weighted-regression residuals were combined with the estimated effect of the disease status (to preserve the estimated effect of disease on expression); in the main text, we refer to this as expression data that is adjusted for all other covariates “conditional on diagnosis”. This procedure yields a normalized and adjusted gene expression matrix carried forward for eQTL and network analyses.
