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Setting fix_formula with variables #281

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UniAlberta opened this issue Aug 30, 2024 · 1 comment
Open

Setting fix_formula with variables #281

UniAlberta opened this issue Aug 30, 2024 · 1 comment
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@UniAlberta
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Hi, I`m using Ancombc2 to find differentially abundant taxa in microbial communities under different treatments. I see here: https://www.bioconductor.org/packages/release/bioc/vignettes/ANCOMBC/inst/doc/ANCOMBC2.html. You have multiple variables in fix_formula, and your variable of interest is bmi. Is it fine if fix_formula is set only to the variable of interest, not all variables in metadata? like this:
output = ancombc2(data = tse, assay_name = "counts", tax_level = "Family",
fix_formula = "bmi", rand_formula = NULL,
p_adj_method = "holm", pseudo_sens = TRUE,
prv_cut = 0.10, lib_cut = 1000, s0_perc = 0.05,
group = "bmi", struc_zero = TRUE, neg_lb = TRUE,
alpha = 0.05, n_cl = 2, verbose = TRUE,
global = TRUE, pairwise = TRUE, dunnet = TRUE, trend = TRUE,
iter_control = list(tol = 1e-2, max_iter = 20,
verbose = TRUE),
em_control = list(tol = 1e-5, max_iter = 100),
lme_control = lme4::lmerControl(),
mdfdr_control = list(fwer_ctrl_method = "holm", B = 100),
trend_control = list(contrast = list(matrix(c(1, 0, -1, 1),
nrow = 2,
byrow = TRUE),
matrix(c(-1, 0, 1, -1),
nrow = 2,
byrow = TRUE),
matrix(c(1, 0, 1, -1),
nrow = 2,
byrow = TRUE)),
node = list(2, 2, 1),
solver = "ECOS",
B = 10))

@Maggie8888
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Yes. It is fine as long as you believe the model is correctly specified.

@Maggie8888 Maggie8888 added the invalid This doesn't seem right label Sep 27, 2024
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