Do you have to normalize microbiome abundance data prior to running an NMDS ordination? I am getting very confused. In the data processing stage, I subsampled the OTU table to a certain read count (this is normalization/rarefying?). Do I normalize the data again prior to running an nmds? In the phyloseq tutorial it gives this code:
#normalization
total = median(sample_sums(WWTF))
standf = function(x, t=total) round(t * (x/sum(x)))
WWTF = transform_sample_counts(WWTF, standf)
WWTF
however, I wanted to run my nmds in vegan so I could also do an envfit and I'm not sure what the above code is doing. Any help would be appreciated!
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