BIOM export to load in R

User Questions
1

Hello,

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

Screen Shot 2016-10-10 at 8.54.24 PM.png1006×76 15.2 KB

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

Screen Shot 2016-10-10 at 8.54.53 PM.png1266×394 27.8 KB

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

Screen Shot 2016-10-10 at 8.58.35 PM.png1594×520 53 KB

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.

2

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?