I have a question regarding the metastats function in mothur.
I would like to analyze the differential abundance of the taxa (output of the phylotype command - I’m unable to do the cluster.split due to restricted computational resources) in my groups. For this purpose, I found the metastats function. In the documentation, I found that the function can determine differential abundance for two different groups at a time.
My question is the following:
Can I use the metastats function to do the differential abundance analysis for 4 different groups?
If so, how would you recommend me to do this?
( I found the following article suggesting in their discussion to replace the t-test by a one-way anova)
I personally do not use metastats since I saw this one here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4727335/
BUT this is just me, ok? I dont want to piss people off who may have good reasons to use metastats. So I apologize in advance if I have insulted any metastats fans!
I would advise you to look into DESeq and indicspecies. Both can be done with imported OTU tables in R and as far as I remember, they coplement nicely each other (because they do comparisons based on different hypotheses) and yes I think you can have more than 2 groups
metastats is pretty limited in that it’s effectively a non-parametric t-test. you’d be better off with lefse or doing your own test in R.
@pschloss Thank you very much for your reply. I got exactly what I needed from lefse! For the sake of learning and being thorough, I also analyzed the data with DESeq2 (thank you @sapou for your help).
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