I am posting this because I have something I want to ask.
I want to create an LDA score (log 10) using r with data obtained with mothur.
However, in my case, I think I need to create a design file by specifying at least 6 or 15 groups for each sample. When I create a design file like this, the classes are not distinguished in the Lefse file. In order to create a Lefse file, do I need to create only two groups in the design file? And what should I do if, like me, I want to divide the data into 6 or 15 groups and create a graph?
Should I group them into two groups and start from the first step, the fastq file?