BIOM export to load in R


I would like to export functional table (KEGG, INTERPRO2GO, …) in a biom format to be able to use with R.

I first check the table with biom-validate

but then when I tried to load the biom table in R I got the following message:

I also tried with another dataset and I was able to load the biom table into R:

It seems like because some KO are shared among several pathways it does not accept duplicates ids. Any idea how to format the biom table to solve that? Add a random id?

Thanks a lot for your help.

The best way to address this is to uncollapse the KEGG tree down to the pathway level only, not to the KO level, using the Tree->Collapse at Level… 3 menu item. When then exporting BIOM1 format, the IDS should be unique.
Does that work for you?