Maggie8888
commented
5 months ago Hi Kris, You should check if the variables you choose to be included as fixed effects have the exact same variable name as "Months_since_construction", "description", "Nitrite.as.N.Sol.mg.kg." and, "Total_HC_C9_C40.sum.mg.kg." in your data.
Hi, I'm new to Ancom-BC2 and I have been trying to run Ancombc2 on a tse that was coerced from a phyloseq object. I'm currently getting the following error and warning messages Error in
[.data.frame(ss_flag, fix_eff) : undefined columns selected In addition: Warning messages: 1: In for (i in seq_len(n)) { : closing unused connection 11 (<-L-2H2ZHH3:11615) 2: In for (i in seq_len(n)) { : closing unused connection 8 (<-L-2H2ZHH3:11615) 3: In sqrt(var_hat) : NaNs produced 4: In pt(abs(W), df = dof, lower.tail = FALSE) : NaNs producedwhen I checked ss_flag and fix_eff both had values of NULL
Here is a copy of the code I am running anbc_test = ancombc2(data = bp7_tse, assay_name = "counts", tax_level = "Genus", fix_formula = "Months_since_construction + description + Nitrite.as.N.Sol.mg.kg. + Total_HC_C9_C40.sum.mg.kg.", rand_formula = NULL, p_adj_method = "holm", pseudo_sens = TRUE, prv_cut = 0.10, lib_cut = 1000, s0_perc = 0.05, group = "description", struc_zero = FALSE, neg_lb = FALSE, alpha = 0.05, n_cl = 2, verbose = TRUE, global = FALSE, pairwise = TRUE, dunnet = FALSE, trend = FALSE, 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 = list(fwer_ctrl_method = "holm", B = 100), trend_control = NULL)
I would greatly appreciate any help on this matter.