I have 12 samples with three replicas each, 36 samples altogether.
In Permanova, if I am not mistaken, it shows n=9 for the rest samples except the control week1 and so on. It sounds confusing! I expected n=3 'cus I have three replicas for each sample. Could you please guide me?
This analysis compares a reference group with all remaining groups. These comparisons are based on pairwise comparisons, so if you compare the group reference with itself, you will only have 3 pairwise comparisons. When you compare different groups (3vs3), you will have 9 pairwise comparisons. So those n’s shown in the xticks are actually the number of pairwise comparisons with the reference group, not the number of samples per group.
Hope this helps,
Your explanation is right! But there is no place to compare one sample with other samples one by one! Can you tell me how can I do that?
I believe that’s your distance matrix, isn’t it?
It is called unweighted_unifrac_distance_matrix.qza file. I think you are right!
I tried with --p-pairwise and --p-no-pairwise parameters but the result is the same! not changd.
Is there someone to give me a clue?