Phyloseq Object have 0 in OTU table

lingvv commented 10 months ago

Hello! Thank you for creating this helpful tool; it has been truly beneficial.

I would like to confirm if it's expected for my phyloseq object to contain all zeros in the OTU table. I am certain that my OTU table is not empty. Thank you for your assistance.

My phyloseq object

phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 1663 taxa and 48 samples ]
sample_data() Sample Data:       [ 48 samples by 4 sample variables ]
tax_table()   Taxonomy Table:    [ 1663 taxa by 7 taxonomic ranks ]
phy_tree()    Phylogenetic Tree: [ 1663 tips and 1656 internal nodes ]

jbisanz commented 10 months ago

Is it actually all zeros, or is that just the first set of values shown in that preview? You should probably check the sum, rowSums, and colSums of your table.

lingvv commented 10 months ago

I've examined my phyloseq object using taxa_sums(ps) [1:10], and it appears not to be empty. My apologies for any confusion caused, and thank you for your prompt response!

However, if you wouldn't mind, could you also provide a guidance to this question? https://github.com/jbisanz/qiime2R/issues/57
Your assistance is greatly appreciated.

> taxa_sums(ps) [1:10]
35e6f4ecc89cd35bd8cc71e6b6a5e87d 
                               2 
6af84e470dc6b2f69701b4e9bcf525d6 
                               9 
73799d5308d251a337e717da4604a2b8 
                               5 
3967519d7c2705c72c8884b7f3a34edb 
                              21 
c0791b6e15722cc74e740ecf4e62fe8a 
                              64 
24ccde73595ce75382cd60122d05b774 
                              64 
988228c6d9b56d5f03225e60d406a64e 
                              28 
22b9fb3d47b0ce3b1adad22497f8258e 
                               5 
a03e5bdad15ab78ea408f5a2ed816d52 
                               6 
02c5af34088fb0b9cd27b8fcea1856c9 
                               4

jbisanz / qiime2R

Phyloseq Object have 0 in OTU table #56