I am running corr.axes and it seems to not to like the inclusion of any categorical data in the metadata file (cannot convert to a float), so I cut that out but my continuous data has missing values. It doesn’t like “na” or just leaving it empty, so I’m wondering what is the best way to handle those. I’m running 1.42.0
I’d probably suggest using
remove.groups to remove those groups that you don’t have the metadata for. Alternatively, you could do the correlation analysis outside of mothur using something like R, which is better set up for dealing with NA values.
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