Unweighted Unifrac Significance Analysis


I’m trying to run the diversity core metrics package on my data and when I run this command:

 qiime diversity beta-group-significance --i-distance-matrix 56900-stomp/unweighted_unifrac_distance_matrix.qza --m-metadata-file stomp-metadata.csv --m-metadata-category Treatment --o-visualization 56900-stomp/unweighted-unifrac-treatment-sig.qzv

It gives my a n= more samples than what I have and don’t know why. Can someone explain me what it does? I already did other PERMANOVAs on my data in R and never bumped into this numbers.

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Hi @Vanessa_Fernandes! Can you send me your unweighted_unifrac_distance_matrix.qza and stomp-metadata.csv files? Also, how many samples are you expecting to be included in the analysis, and how many samples are you seeing in your R analyses?