Normalisation of Microbiome Data for Beta Diversity Analysis

Question

[qwrissie]

I am looking for methods to normalise the read counts in an OTU table prior to beta-diversity analyses and hierarchical clustering of samples. I want to avoid rarefying because some samples have very low reads counts and this would therefore greatly increase error. Converting to a percentage would ignore the differences in variance between samples. Can anyone recommend any other methods?

[sridhar56]

Have you tried phyloseq for the same purpose?