Dear Bonnie,
limma has no difficulty with continuous predictors, but they are not permitted to include missing values. Your continuousVar apparently contains missing values.
BTW, neither lmFit() nor model.matrix() have an argument 'na.action', so it has no effect in the calls you give below.
Best wishes
Gordon
Dear Bonnie,
The issue isn't so much between linear and logistic regression, as between differential expression (in the outcome is used to explain expression, as in limma) and prediction (in which expression is used to explain the outcome).
I don't work on prediction and can't recommend packages.
Best wishes
Gordon
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