AMOVA and HOMOVA design file set-up

Good Day Forum,

I’m trying to make sure my design files are set-up properly. I have a Diet x Treatment x Sex factorial experiment and have come to the conclusion I have to analyze each factor separately for AMOVA and HOMOVA. Below are examples of my codes.


Here are examples of my set-up. Can someone confirm if I’m on the right track with my set-up in the file?

group diet
1Colon Sucrose
2Colon Sucrose
3Colon Fructose
4Colon Fructose
5Colon Malto
6Colon Malto

group treatment
1Colon PBS
2Colon PBS
3Colon Shigella
4Colon Shigella
5Colon PBS
6Colon Shigella

That looks right for using amova and homova in mothur. If you’re an R-user you should try adonis in the vegan package as a replacement for amova. It can handle the two-factor design. If you go that route you will need to provide a formatted distance matrix like so, otherwise Bad Things Will Happen…

dist <- read.table(file=“my_square_distance_matrix.dist”, header=F, row.names=1)
thetayc <- as.dist(dist)
thetayc.adonis <- adonis(thetayc~md$SP*md$Sex)

Thanks for confirming.