Help with understanding phyloseq outputs

Hello everyone! I am having trouble understanding some of my output results. This in an example of one of them:

Response temp_ celsius:
Df Sum Sq Mean Sq F value Pr(>F)

Shannon 1 501 500.98 4.9044 0.03167 *

Residuals 47 4801 102.15

Can I correctly assume that my Shannon H is F value=4.9044 and that my p value is Pr(>F)=0.03167? If so, are these both needed to take in consideration when establishing possible interpretation of results?

Welcome to the forum, @Albert!
It’s not clear to me what these results are, or what you’re asking. Would you mind posting the command you ran, and maybe a screenshot or Artifact so it’s clearer what you’re looking at?

Chris :fish:

Hi Chris!

I am observing how diversity can be possibly affected by temperature. So I plotted richness against temperature using:

Estimate_richness(physeq1, measures=c(“Shannon”,”Simpson”)) thengeom_smooth()using formula “y ~ x’

My output results are those mentioned in the previous post. Therefore, my question is the F value=Shannon H? And Pr(>F)= p value?

I provided a visualization in case that helps.

Hi @Albert,
It looks like you are using phyloseq, not QIIME 2, so I have reclassified this topic to “other bioinformatics tools” and altered the title for clarity. Some other users on the QIIME 2 forum are familiar with phyloseq and may be able to offer help, but otherwise I recommend reading the phyloseq documentation and using its support forum (github issues?) to get more direct help.

No, this looks like an F-statistic — you should check the phyloseq documentation for a better description of what test is being run by “Estimate_richness” and how to interpret.


Good luck!

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