I have a naive question regarding the CLR transformation for compositional data, more specifically on microbiome relative abundance.
I have normalised the raw counts of my OTUs (gathered by genus) by a TSS and then I would like to perform a CLR on it.
In this OTU dataset, I have a “Unclassified” column corresponding to non-affiliated genus and I am not interested by this column, I therefore ask myself if I should perform the CLR before or after removing the Unclassified column.
For me I should perform the CLR on the “complete” compositions but I wonder if there could be an impact on the analysis if I do it on a sub-composition since a proper CoDA should be sub-composition coherent…
Thank you for your help