#45 is really weird #120
Description
I think all the discussions under question # 45 did not address the root of the problem. Firstly, it needs to be clarified that the problem itself should be "Error in purrr:: map()"
ℹ In index: 1.
Caused by error in svd():
! ' There are infinite or missing values in x ',
It's not about bootstrap, these should be two separate issues. Secondly, this error is quite strange because I only set different seeds (123yes, 111no), which may cause errors when running.
below is my code:
otu <- read.csv("otu.csv",row.names = 1)
env <- read.csv("env.csv",row.names = 1)
tax <- read.csv("tax.csv",row.names = 1)
tax <- as.matrix(tax)
physeq <- phyloseq(
otu_table(otu,taxa_are_rows = TRUE),
tax_table(tax),
sample_data(env)
)
physeq
set.seed(111)
data <- normalize(physeq, method = "rarefy")
adj <- tax_table(data) %>% apply(.,2,function(x) length(unique(x))) %>% sum
lefse <- run_lefse(
data,
norm = "none",
group = "grazing",
multigrp_strat = TRUE,
wilcoxon_cutoff = 0.05,
kw_cutoff = 0.05,
bootstrap_n = 50,
lda_cutoff = [1]
)
below are my data
Uploading env.csv…