limma wsva() does not return what it says it will
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Jenny Drnevich ★ 2.0k
@jenny-drnevich-2812
Last seen 1 day ago
United States

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!

limma • 748 views
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@gordon-smyth
Last seen just now
WEHI, Melbourne, Australia

Thanks for the heads-up. I've corrected the help page now. (Earlier versions of the function did output the whole augmented design matrix instead of just the surrogate variables.)

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