FrederickHuangLin
Error in `[.data.frame`(ss_flag, fix_eff) : undefined columns selected
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 produced
when 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.
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.
