Hey,
I've been trying to get the ancombc2 to run for me, i am new to using ancombc. I have 3 study groups that i would like to compare with pairwise but I keep running into an error:
Error in names(x) <- value :
'names' attribute [3] must be the same length as the vector [2]
the pairwise works fine if it have pseudo_sense = FALSE but once im setting it to TRUE, it doesnt work anymore.
I used debug to see where the error occurs and found its from this line:
colnames(ss_flag_pair) = pair_col_name and they do indeed not match up, however, i have no idea how to fix this issue.
the ss_flag_pair only contains two of the studyarms, whereas pair_col_name has all three. when i looked at how they are both made, it seems that its only the 2 study arms as the it is the refernce group, but im not sure if thats the right conclusion/reason.
output_pw1 <- ancombc2( data = ancom_phyl, tax_level = "Species", fix_formula = "studyarm", group = "studyarm", p_adj_method = "BH", pseudo_sens = TRUE, prv_cut = 0.10, struc_zero = TRUE, neg_lb = FALSE, global = TRUE, pairwise = TRUE, mdfdr_control = list(fwer_ctrl_method = "holm", B = 100) )
I would greatly appreciate any insights or suggestions on how to resolve this issue. Thanks in advance for your help!