CLR transformation

Dear mixOmics team,
Thank you for your useful package.

I have 2 naive questions regarding the CLR transformation for compositional data.

  • If I want to remove “rare” OTUs on the basis of relative abundance (eg: <0.5%), do I have to CLR-transform my data and then remove them with a filtered list on the basis of relative abundance ? or do I delete them before transforming my table?

  • If I want to work at the genus scale (aggregate my OTUs to the same genus), can I sum the CLR abundances of corresponding OTUs or should the CLR be better applied on the aggregated relative abundance table at the genus scale?

Thank you for your answers and have a nice day

hi @Callie

1 - we recommend you follow our guidelines here:, i.e. remove the rare OTUs then CLR transform after adding an offset.

2 - You should first aggregate, then CLR transform (I think).