After filtering down dataset based on sequencing batch and specific T6 timepoint, I tried to do an ancombc2 comparison between 2 groups on a Phylum tax level:
out_phylum_S2022_T6 <- ancombc2(
data = tse_S2022_T6,
tax_level = "Phylum",
fix_formula = "responder",
p_adj_method = "holm",
pseudo = 0, pseudo_sens = TRUE,
prv_cut = 0, # no prev filtering necessary anymore
lib_cut = 0,
group = NULL,
struc_zero = FALSE,
neg_lb = FALSE,
alpha = 0.05,
global = F,
pairwise = FALSE,
dunnet = FALSE,
trend = FALSE,
n_cl = 1,
verbose = TRUE,
iter_control = list(tol = 1e-5, max_iter = 20,verbose = FALSE),
em_control = list(tol = 1e-5, max_iter = 100),
lme_control = NULL, mdfdr_control = NULL,
trend_control = NULL
)
Following output is generated in console: Error in { : task 1 failed - "'fmt' length exceeds maximal format length 8192"
The same analysis was done on tax_level="Genus" and tax_level="Species" without errors. Is there any specific solution for tax_level="Phylum"?
BR, Dora