# About metastats for multiple groups **URL:** \ **Category:** Commands in mothur\ **Created:** [June 4, 2020, 8:45am UTC](https://forum.mothur.org/t/about-metastats-for-multiple-groups/20555 "2020-06-04T08:45:23Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![Bapt](https://avatars.discourse-cdn.com/v4/letter/b/0ea827/32.png) [@Bapt](https://forum.mothur.org/u/Bapt)\ **Post date:** [June 4, 2020, 8:45am UTC](https://forum.mothur.org/t/about-metastats-for-multiple-groups/20555/1 "2020-06-04T08:45:23Z")
Hi, 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) > **[Statistical Methods for Detecting Differentially Abundant Features in...](https://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1000352)** > > Author Summary The emerging field of metagenomics aims to understand the structure and function of microbial communities solely through DNA analysis. Current metagenomics studies comparing communities resemble large-scale clinical trials with... ---
**Author:** ![sapou](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/sapou/32/164_2.png) [@sapou](https://forum.mothur.org/u/sapou)\ **Post date:** [June 4, 2020, 10:51am UTC](https://forum.mothur.org/t/about-metastats-for-multiple-groups/20555/2 "2020-06-04T10:51:59Z")
Hey Bapt I personally do not use metastats since I saw this one here [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4727335/](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 Good luck ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [June 4, 2020, 7:53pm UTC](https://forum.mothur.org/t/about-metastats-for-multiple-groups/20555/3 "2020-06-04T19:53:07Z")
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. ---
**Author:** ![Bapt](https://avatars.discourse-cdn.com/v4/letter/b/0ea827/32.png) [@Bapt](https://forum.mothur.org/u/Bapt)\ **Post date:** [June 8, 2020, 7:30am UTC](https://forum.mothur.org/t/about-metastats-for-multiple-groups/20555/4 "2020-06-08T07:30:23Z")
@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). ---
**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\ **Post date:** [June 18, 2020, 7:30am UTC](https://forum.mothur.org/t/about-metastats-for-multiple-groups/20555/5 "2020-06-18T07:30:24Z")
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