Hello ! Folks.
I'm trying integrate OTU table data from different batches.
Hence, I'm considering to do normalization before any further analysis.
I have looked through normalization methods and found that Centered Log ratio was one of the most mentioned method.
(I know it is built in many plug in of qiime. But I have to do other analysis in addition to the functions in qiime2)
However, I found that a sentence saying "Make Pseudocount before CLR"). Is there any pre-step before do CLR transformation ? Or the pseudocount would be made in the normal process integrated in CLR transformation ? I will use R, ALDEx2 package / or Python sckit-bio package to do my table transformation to CLR form.
Please suggest me and explain me about the question.
Many thanks for your help.