I have several OTU tables from each study raw data. What I want to do is to compare 2 different OTU tables so as to get some information whether there is a difference between studies under different situation.
So, I’ve been searching some ways to do so but I’m not sure if it is right and some didn’t work…
Here are the way I tried. or I will try
I get a ratio of each OTU value by total OTU value from merged table of two studies and did a nomalization using scale() in R afterwards. I think this is the right way but I’m not sure…
Just merge two clustered table using QIIME2 and then do qiime feature-table rarefy. And do taxonomy analysis afterwards with the rarefied table.
Is there a better way to do so…? or if ways I did are wrong, please let me know…
Option 2 is the method that's currently available in QIIME 2, and is perfectly adequate for what you are trying to do.
Pretty much any method in QIIME 2 that requires normalization (alpha diversity, beta diversity, differential abundance) has that normalization built in, so in general no normalization needs to be performed prior to running that method.
So just merge those tables and rarefaction is built in for alpha/beta diversity tests. Other normalization is used by differential abundance methods (ancom, gneiss).
This is a contentious area of research, though. Feel free to normalize with your favorite method and then import and merge your tables, your protocol sounds fine (though I don't know what scale() does so cannot comment on that aspect).
don't use the rarefied table for any taxonomy analyses. Relative frequency is fine for visualizing composition, e.g., as bar plots. Differential abundance tests do their own normalization.
