Using limma within Bioconductor here, which is a linear model package for microarray data and lmFit on gene expression data, I can perform a series of regressions gene ~ covariates by specifying design = model.matrix(~ covariates) and calling lmFit(eset, design).

How can I instead run the regressions phenotype ~ gene + covariates?

  • $\begingroup$ I think you can ask this question better at bioc support site. There the developers of limma can answer you. $\endgroup$
    – benn
    Apr 17 '19 at 7:49

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