I’m having a similar issue. I’d like to export the feature table as a .csv, but it only gets exported as a .biom file, which doesn’t seem to be compatible with phyloseq:
I’ve tried to import it two ways:
rich_sparse_biom = system.file("extdata", "/Users/annaknight/Documents/Microbiome/exported250/feature-table.biom", package = "phyloseq") > rich_sparse = import_biom(rich_sparse_biom, parseFunction = parse_taxonomy_greengenes) Error in read_biom(biom_file = BIOMfilename) : Both attempts to read input file: either as JSON (BIOM-v1) or HDF5 (BIOM-v2). Check file path, file name, file itself, then try again. biom_file="/Users/annaknight/Documents/Microbiome/exported250/feature-table.biom" biomot = import_biom(biom_file) Error in dimnames(x) <- dn : length of 'dimnames'  not equal to array extent In addition: There were 50 or more warnings (use warnings() to see the first 50)
Do you have any suggestions on how to fix this/export as tsv/csv?