I'm trying to use DESeq2 to determine if an OTU is enriched by treatments from 16S rRNA sequence data.  I imported OTU counts for each library (otu), and metadata information for each library (meta).  One of my metadata columns is a factor with 5 levels (factors).  I want to do all pairwise comparisons for all 5 factor levels.

I've tried to do it this way:

dds = DESeqDataSetFromMatrix(countData = otu, colData = meta, design = ~factors, betaPrior = FALSE)

The rownames in my metadata are the same as the colnames in the otu table, but I get an error:

Error in FUN(X[[i]], ...) :   assay colnames() must be NULL or equal colData rownames()

I also tried using phyloseq this way:

dds = phyloseq_to_deseq2(phyloseq(otu,meta), design = ~factors)

dds = DESeq(dds, design = ~ factors)

This method only compared the first and last factor levels, but I want all the comparisons.

I need help with the syntax for the contrast argument.

Thanks!