Thank you very much for this great tool to achieve easily multivariate analyzes in microbiome studies.
I still do not fully understand which parameters in my dataset can help me to choose the good method of normalization or or transformation.
I used rarefied dataset with relative abundance with about 150 different samples (not related, one time point). I want to compare healthy (n=67) vs patients (n=125). In another analysis, I want also to compare within patients different metadata (with some values presented in 5 to 100 patients).
From the paper by Weiss et al, (Microbiome, 2017), I make the asumption that using rarefied data, I may not need further normalization. Do you think I am wrong ?
I tried several methods of transformation, with various results from one to another that puzzled me. Comparing to a more linear analysis with LEFSE, I found that the closer method was using AST transformation with no other normalization applied.
Do you have any insights that can give me a proper method to define properly the settings I have to use in my analysis and which parameter I have to take into account to do so?
Thank you very much,