Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

lefse analysis error #111

Open
KOMALSKK opened this issue Jan 17, 2024 · 0 comments
Open

lefse analysis error #111

KOMALSKK opened this issue Jan 17, 2024 · 0 comments

Comments

@KOMALSKK
Copy link

Hello, Can you help me with the following error. I created a phyloseq object physeq and performed lefse.

library(microbiomeMarker)
norm_tss(physeq)
normalize(physeq, method = "TSS")

data(physeq)
mm_test <- normalize(physeq, method = "CPM") %>%
run_lefse(
wilcoxon_cutoff = 0.01,
norm = "none", # must be "none" since the input has been normalized
group = "type",
kw_cutoff = 0.01,
multigrp_strat = TRUE,
lda_cutoff = 2

But I get the following output;
mm_lefse <- run_lefse(

  • physeq,
  • wilcoxon_cutoff = 0.05,
  • group = "type",
  • kw_cutoff = 0.05,
  • multigrp_strat = TRUE,
  • lda_cutoff = 2
  • )
    Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
    Also defined by ‘tidytree’
    Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
    Also defined by ‘tidytree’
    Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
    Also defined by ‘tidytree’
    Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
    Also defined by ‘tidytree’
    Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
    Also defined by ‘tidytree’
    Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
    Also defined by ‘tidytree’
    Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
    Also defined by ‘tidytree’
    Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
    Also defined by ‘tidytree’
    Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
    Also defined by ‘tidytree’
    Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
    Also defined by ‘tidytree’
    Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
    Also defined by ‘tidytree’
    Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
    Also defined by ‘tidytree’
    Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
    Also defined by ‘tidytree’
    Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
    Also defined by ‘tidytree’
    Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
    Also defined by ‘tidytree’
    Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
    Also defined by ‘tidytree’
    Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
    Also defined by ‘tidytree’
    Error: Too small samples in each class or the variance of feature abundances within a class too small (zero or near zero).

Can you help me finding the error, here.

Thank you.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant