Hi all,

I am new to the use and interpretation of qiime results. Perhaps the answer is obvious, but after I reading the answers in the forum it is not clear to me yet.

I ran the beta diversity metric and I got the following results:

unweighted_unifrac_distance matriz. qza

unweighted_unifrac_pcoa. results. qza

unweighted_unifrac_emperor. qzv

weighted_unifrac_distance matriz. qza

weighted_unifrac_pcoa.results. qza

weighted_unifrac_emperor. qzv

jaccard_distance matriz.qza

jaccard_distance pcoa.results.qza

jaccard_distance emperor.qzv

bray_curtis_distance matrix.qza

bray_curtis_pcoa. results.qza

bray_curtis_emperor.qzv

I am trying to replicate this in R, but it is not clear to me the difference between the three files it throws at me for each index, example: I have three results for unweighted_unifrac

unweighted_unifrac_distance array. qza

unweighted_unifrac_pcoa. results. qza

unweighted_unifrac_emperor. qzv

I should use the unweighted_unifrac_distance array file. qza to make the box and whisker plots ?; the file unweighted_unifrac_pcoa. results. qza is the one that I must export to R to obtain the same results that I see in the unweighted_unifrac_emperor file. qzv or just the emperor visualization is enough and can I use that PCOA chart for my analysis?

I will take the opportunity to ask another question: I am working with the lung microbiome in three groups of studies: (HIV + pneumonia, pneumonia without HIV and HIV without pneumonia), I obtained these results in the Shannon index and I do not know if the values are correct, can you have high values in this index?

Sorry for so many questions, I am new and I am trying to learn from this forum. Sorry also for my english, it is not my first language

I'd appreciate your help

Thanks

Katherine