KW/Wilcoxon tests stratification

[jwframe28]

Hi all,

We want to cite lefse as a paper in our methods and have 2 questions. Your paper says that:

"The factorial KW rank sum test is applied to each feature with respect to the class factor; the subclass and subject information are used as stratifying subgroups when present."

Does this refer to the KW test? because in the code it only looks like there's a comparison between classes (and subclass is only taken into account in the Wilcoxon step portion; while subject is used in the LDA model)

And finally, if there is not subclass, is the Wilcoxon test performed between classes or skipped altogether?

Thanks so much, great tool you guys have here!!!

Best,
John