I understand NaNs are missing data but I am not sure where this has arisen from.
The code however works if I use one of the unmerged files below. ie replace longitudinal_merged_table.qza with table_1.qza or table_2.qza or table_3.qza or table_4.qza (see below).
I therefore am
guessing I haven't merged the files correctly, though from looking on the qiime2 forum I think I have used the recommended method.
Any suggestions and help much appreciated! Let me know if you need any further information.
Thanks!
I've had a look through these already for merging and trying to work out why the beta diversity hasn't worked but I am still at a loss, apologies I am not a true bioinformatician. https://docs.qiime2.org/2018.8/tutorials/fmt/
Basically I had a few samples in that file that were retained in the table.qza file but none of the reads for those samples had met the requirements during the qiime dada2 denoise-paired step.
If I created a new column in my metadata file called ‘fail’ with variables ‘y’ and ‘n’ and then used the command:
qiime feature-table filter-samples https://docs.qiime2.org/2019.10/plugins/available/feature-table/filter-samples/
to filter out all those sample which failed during the qiime dada2 denoise-paired step calling them ‘n’ in metadata column ‘fail’.
Once these are removed the filtered table runs in qiime diversity beta without a glitch.
Not sure if there is a less roundabout way of doing this but this is a fix if anyone is having a similar problem.