pseudo-F ratio in PERMANOVA test

General Discussion
1

Hi, could someone, help me to understand better about value for pseudo-F ratio in PERMANOVA test?

Question:
Should I also need to consider the pseudo-F ratio value while doing PERMANOVA test even if I get the significant p-value or q values? Is there any meaning behind larger or smaller pseudo-F ratio?

For example, in case 1 and case 2 result is significant based on q-value but pseudo-F ration is different? What does smaller (3.459) and larger pseudo-F ratio (66) means?

Case 1
Group1 Group 2 Sample Size Permutations pseudo-F p-value q-value
Local Remote 300 999 3.459 0.003 0.004
Case 2
Group1 Group 2 Sample Size Permutations pseudo-F p-value q-value
Local Remote 300 999 66 0.003 0.004

Thank you.

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2

Hi @skhanal999,
You can think of the pseudo-F as a measure of effect-size and is different than your p value. The larger your pseudo-F the greater the difference in your comparison. I would recommend reading more about the test and what it does here.

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3

Thank you Mehrbood for explanation. I will see the link you suggested.

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