I've started to play around with limma's new wsva() function to generate surrogate variables. The help page says under Value: "Numeric matrix, same as design but with n.sv columns added containing the surrogate variables.". However, the actual value returned is just the surrogate variables, not the original design matrix plus the surrogate variables. It's no problem to add them myself, but I thought I'd point out the inconsistency.

Thanks for always expanding and adding new functionality!