My apologies in advance, I am not a statistician and do not know much about advanced statistical analysis.
Study Design: I am trying to compare microbiome from two sites, let's say, palm and elbow.I have both palm and elbow data from 8 different subjects. Since my data is matched by a subject, I guess we cannot use PERMANOVA as the data is not independent (Correct me if I am wrong).
What would be the best way to go about this study? Finding insights into intra sample variation would be helpful (Eg. Subject 1's Palm microbiome vs. Subject 1's Elbow Microbiome) but some global information (Across all microbiomes) will also be very helpful.