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Thread: Option for post-hoc test after permanova for community data?

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    Question Option for post-hoc test after permanova for community data?




    Hi there,

    Thank you for reading my post and hopefully someone can provide me with some help!

    For my master's thesis, I have used microbial community identification with QIIME. I have 47 samples spread over 4 different treatments and 4 different time points (2 different years and 2 different seasons), so n=3, except for 1 treatment at the first time point. From QIIME I ended up with 1151 genera, where for at least one sample the abundance of a genus is >0. To be able to handle this data I have set a minimum abundance level of 1% for at least 1 sample, which left me with 37 genera. For this data I have used a central log ratio transformation and created a euclidian based distance matrix, and ran this through a permanova in R with the following model:

    adonis(formula = X ~ Treatment * as.factor(Year) * as.factor(Season))

    From this I get significant results from the factor treatment (p = 0.005) and the interaction between year and season (p = 0.001), as I expected. Now there is no post-hoc test for a permanova, but I am wondering if there is any kind of test that I could do that could tell me which genus/genera are driving this change?

    Thank you in advance for your help!

    Kind regards,
    Bobby

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    Re: Option for post-hoc test after permanova for community data?

    You can use simper() in the vegan package. This will give you a decomposition of how much each genus is contributing to the similarity between groups.
    The earth is round: P<0.05

  3. The Following User Says Thank You to bugman For This Useful Post:

    Bob3 (02-24-2016)

  4. #3
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    Re: Option for post-hoc test after permanova for community data?

    Thank you! I have been working with it and struggling to figure it out for a little while, but I've got it. Thank you for your advice!

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    Re: Option for post-hoc test after permanova for community data?


    Thanks for following up Bob3.

    Often posts are left hanging without resolve. Glad to hear you got it sorted out!
    The earth is round: P<0.05

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