Can we use ANOVA to calculate the p value for PCoA analysis instead of PERMANOVA or ANOSIM test?

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Jose Pedro Canavate

Principal coordinate analysis (PCoA) is an ordination unconstrained multivariate analysis. It does not test for significance, so you need either ANOSIM or PERMANOVA to know the significance of your multivariate data set. I use PRIMER software for this kind of analysis. It is easy to operate.

Sadia Kanwal

Jose Pedro Canavate Thanks alot.

Syed Abdul Rehman Bukhari

Q:Can we calculate p value of PCoA using SPSS or graphpad prism? Which test is recommended for PCoA analysis?

PCoA does not require to have p values and yes you can use SPSS for PCoA but you will have to use a separate utility known as MonteCarlo.exe which gives comparative eigenvalues for you PCA.

After obtaining factors with eigenvalues greater than MonteCarlo.exe you can perform ANOVA to find out significance within and between groups.