Hi,

I have analyzed my metagenome data with phyloseq and used the R package biom to output a biom file containing my phyloseq normalized and filtered data.  I need to run a statistical test in Qiime.  My biom file generates an error that appears to be a column name problem for 'id'.  As best I can determine, the source of the problem is that my biom file is formatted in the old version 1.4 json, and qiime requires version 2 hdf5 format.  I have repeatedly tried the biom convert command recommended here, http://biom-format.org/documentation/biom_conversion.html.  Can someone please help me with the correct conversion method to convert from the R biom file to a format accepted by qiime?

Susan

biom is a CRAN package, you should directly write to the respective CRAN mailing list or to the authors of the package.

There exists as well a vignette for the biom package: https://cran.r-project.org/web/packages/biom/vignettes/biom-demo.html