Applying the run_lefse command.

[ricmedveterinario]

Hello. I'm having a little strange result,

When I use the "run_lefse" command, one of the groups (only two groups) is being pointed to the Bacteria kingdom prominently.

This is normal? how can I explain

#commands
lef_out_M <-run_lefse(ps02, group = "taq", norm = "CPM", kw_cutoff = 0.05, lda_cutoff = 2,
wilcoxon_cutoff = 0.01)
bar_lefse_M <- plot_ef_bar(lef_out_M,label_level = 1, max_label_len = 60)

[fconstancias]

Hi @ricmedveterinario,

I am experiencing a similar behaviour using run_deseq2 on some data. k__Bacteria is identified altough all ASV are assigned to Bacteria in my phyloseq object.

@yiluheihei, how should we interprete that?

[ricmedveterinario]

Hi @fconstancias,

I'm still not knowing how to deal with this, just like you.

Probably there may be some classification error in the data and thus a difference in the taxonomic classification at the Phylum level is identified. If not, an error in the microbiomeMarker package.

Just an assumption.
If you discover a solution, please bring it to this topic,

Thanks.

[fconstancias]

Any update on that?