I've been having an issue (I think since an upgrade to R versions > 4.0) where qza_to_phyloseq(features = "table.qza", taxonomy = "silva_132_taxonomy.qza") returns this error:
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘prune_samples’ for signature ‘"array", "phyloseq"’
BisanzLab
commented
3 years ago
I've been having an issue (I think since an upgrade to R versions > 4.0) where
qza_to_phyloseq(features = "table.qza", taxonomy = "silva_132_taxonomy.qza")returns this error:It seems to be an error with phyloseq, possibly related to changes in how matrices are handled in newer versions of R. Simply converting the imported matrix to dataframe before passing it to phyloseq::otu_table() seems to fix the issue.