Hi friends in qiime2,
I used qiime2 and R to generate PCoA matrix on the same beta diversity matrix.
PCoA matrix generated from two methods are different.
Has anyone met the same issue before or does anyone have an opinion on it? Thanks.
Way1. The unweighted UniFrac pcoa was generated in qiime2 using codes below.
qiime diversity pcoa \ --i-distance-matrix $diversity_dir/unweighted_unifrac.qza \ --o-pcoa $pcoa_dir/unweighted_unifrac_pcoa.qza
Then unweighted_unifrac_pcoa.qza was loaded into R using codes below
Way2. The unweighted UniFrac pcoa was generated in phyloseq r package using codes below.
uufp_phy= ordinate(physeq, “PCoA”, “unifrac”, weighted=FALSE)``
Then I compared the
uufp_phy, these two objects are different.