Hi Michael and Sophie, Distances on transformed data still make sense, although Bray Curtis makes much less sense on the transformed counts than several others which are available in phyloseq as you suggest, one can get a pretty good idea of how to proceed by working through the supplementary material of the paper, it has it's own repos at: Also Sophie there is a github thread for phyloseq with deseq at: http://joey711.github.io/waste-not-supplemental/ and https://github.com/joey711 Best Susan