Hi all. I have a set of data that I have analysed with qiime2/2018.2.
All has run OK and I have checked that the metadata file is correctly formatted.
Unfortunately I can’t post some parts of the analysis due to commercial sensitivity but I was hoping for some general feedback on the nature of the problem.
Basically, as mentioned, both Jaccard and Bray-curtis emperor plots don’t show all the samples listed in both the fastq manifest and metadata file, but do show a category called “nan”. We do see a clear separation of the things we think should be separated so the results seem valid, I just don’t understand why I’m putting in 70 samples and only 64 of them are visible, and where this “nan” category is coming from (“nan” shows up as a single category with a single sample but it is not in the metadata file and I’ve checked the formatting of the metadata file extremely thoroughly).
I think I’m running up against the limits of my knowledge of what emperor plots are supposed to show. Can anyone help here?