Utility of rarefy function and rarefaction?


(Sabah Ul Hasan) #1

I see there are already some discussions on this topic in the forum, but that the rarefy function still exists. Copy/pasting from original Github comment:

" I’m unsure if this may be too bold of a comment, but may rarefaction now be obsolete? I’ve been reading a good deal about the artifacts that can arise with rarefying these past few months and perhaps this is a function worth getting rid of as part of the surmounting statistical evidence?

ie https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003531 "


(Nicholas Bokulich) #2

Hi @sabahzero,
Great question! I think it is too early to call rarefaction obsolete, though it is certainly on its way out the door. Your question is a replicate of some previous posts — see this response:

So it is still quite useful to expose functionality that a very large number of users still rely on.

Similarly, QIIME 2 has several methods for OTU clustering, which is still very popular (and useful for some applications), even though denoising methods are theoretically much better.


(Sabah Ul Hasan) #3

Thank you for the quick and thorough reply, @Nicholas_Bokulich! These are helpful to read. I skimmed through some of them, but good to refresh.

Agree it’s popular, but is it correct statistically? That’s where I’m a bit uncertain and agree it may be on its way out.