ThisIsMaggie comments

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                                            ThisIsMaggie

global test and pairwise comparisons giving pvals of all NA or all 1

Could you please provide more information regarding your data?

Error in { : task 1 failed - "values must be length 1, but FUN(X[[2]]) result is length 0"

Could you please check the missingness for the variable "Batch"?

Different results with ancombc2 depending on the order of the taxa

Thanks for your question. Could you please provide more details of your data?

Visualization the output of ancombc2

Could you please provide the information for your res_prim object ?

Interpreting negative lfc values for "intercept" in primary result

The intercept can be ignored since usually that term is not of interest.

R session aborted while running ANCOMBC2

Please try to update all the required packages and restart R studio.

ANCOM_BC2's Global test approach?

Please refer to the link for ANCOMBC2 https://bioconductor.org/packages/release/bioc/vignettes/ANCOMBC/inst/doc/ANCOMBC2.html and the link below for details in terms of the methods https://www.nature.com/articles/s41467-020-17041-7

Models used for DA and binomial outcomes

You may refer to the link https://bioconductor.org/packages/release/bioc/vignettes/ANCOMBC/inst/doc/ANCOMBC2.html for more detailed explanation. We did not use glm framework.

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

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...

ancombc2 output fmt length exceeds maximal format length 8192

Your samples may have an excessive number of zero values if you do not filer them down. This will cause an issue while conducting unbiased estimation.