Hi, I am trying to launch some analysis using the CCREPE package, but I am having some problems.
I am working at the ASVs level, with a dataset of 7 samples that after filtering ASVs, and retaining those that have a relative abundance > 10-4 in at least one of the samples, I am left with around 400-500 ASVs.
This is how I execute it:
ccrepe_output=ccrepe(x=input_reptop_skin_genus, sim.score = nc.score, iterations = 1000, min.subj = 7,verbose = TRUE)
And I get those warnings:
Even more, all the resulting matrix (sim.score, p.values, z.stat, q.values) contain a huge amount of NAs, in the majority of outputs all of them are just NAs.
Please, could you help me to fix those warnings and adjust the parameters properly?
Thanks in advance.