I have been through the forum regarding the “sub.sample” command.
From what I understood, alpha and beta diversity indicators are calculated without prior use of the “sub.sample” command, but with specifying subsample=T (or subsample=xxx) in the commands “summary.single” and “summary.shared” / “dist.shared commands”, respectively. The latter command generates distance matrices that refer to a subsample of the whole dataset (right?), and such matrices are visualized using PCoA, NMDS or used in commands like AMOVA and HOMOVA. In addition, for the commands “corr.axes”, “get.communitytype”, “metastats” etc. one’s need to run the command “sub.sample” first.
Here are my questions:
- if i want to switch to PRIMER to generate NMDS graphs (instead of using MOTHUR , shame on me!), is it correct to run the “sub.sample” + “get.relabund” commands to generate a . relabund file that will imported in PRIMER?
- in the commands “heatmap.sim”, “heatmap.bin”, “venn”, “get.sharedotu” and “get.coremicrobiome”, should I use the “subsampled” dataset (generated with the “sub.sample” command), or the whole dataset ? I think it is the subsampled dataset, but I am not 100% sure.
Thanks for your help,