I am working on the effect of N fertilization on bacterial community composition using 16s rRNA sequencing method in two different soil types. I want to check the individual and interactive effect of N addition and soil types on bacterial community composition. So I need to go for PERMANOVA or PCCA? and what is the main difference between PERMANOVA and PCCA? Thank you.
Hi Sami
Please read the following links
https://fukamilab.github.io/BIO202/06-C-matrix-comparison.html
http://rfunctions.blogspot.com/2016/11/canonical-correspondence-analysis-cca.html?m=1
Hello Sami,
PERMANOVA is used to compare multivariate data of 2 or more groups. It is used to check whether there is any significant difference between 2 or more groups based on the full multi variate profile. For this, a distance between samples is considered.
pCCA, on the other hand is used to identify explanatory variables, which separate the samples in a tranformed multi dimensional space.
These are simple explanations. To know more, you can refer to the internet.
Probably you will need to use both methods because one of them permits you to display graphically your results (PCCA), and the other one shows you if the eventual difference observed in the PCCA is statistically supported (PERMANOVA).
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