Hi everyone! I'm working with ANCOM-BC to analyze differences in microbial taxa between two groups, and I’m trying to understand the results. For some taxa, the diff column is marked as "true," indicating a difference between groups. However, the passed_ss column is "false" for these same taxa.
What does it mean when a taxon shows diff as true but doesn’t pass the subsampling significance (ss) filter? Does this imply that the detected difference may not be reliable? Any insights into interpreting this combination of results would be appreciated!
Thanks in advance!
I’m relatively new to biostatistics and face some difficulties interpreting my results. I’ve read through the manual and the tutorial on the sensitivity analysis for pseudo-count addition, but I’m still a bit unclear on some of the details.
From what I understand, the sensitivity analysis tests how adding different pseudo-counts (values between 0.01 and 0.5) to zero counts in the data affects the results. The idea is to see if the p-values change significantly when different pseudo-counts are used. However, I’m not sure what to make of this in terms of reliability:
If the p-values fluctuate across the different pseudo-counts, does that mean the taxon’s results could be unreliable? Does this suggest that the results might be prone to false positives, where a taxon is incorrectly identified as differentially abundant? I would really appreciate a clearer explanation of how this sensitivity analysis works and what it means for the validity of my findings.
You got it. The taxon with
passed_ss = FALSE
is likely a false positive.In layman's terms,
passed_ss = TRUE
is used for taxa that are always significant no matter you perform pseudo-count addition (because you are including in the differential analysis the zero counts as psedu-count) or use the complete data (excluding directily the zero counts). edit: This done by ancom-bc2 because taxa with lot of zeros (eg rare taxa) can appear significant potentially leading to inflated q-valuesYou can find a more complete explanation in the ancom-bc2 manuscript: Strategies implemented in ANCOM-BC2 to handle zeros
Thank you for the previous answer, it was really helpful!
I have another question regarding ANCOM-BC2. In my analysis results, I came across the variable "passed_ss intercept." Can someone explain what it means when a taxon "passed_ss intercept"? I've noticed that this value can be marked as true or false in different samples. What does this variation mean, and why might it differ across samples?
Any insights would be much appreciated!
Thanks in advance!
columns with the term
intercept
can be ignored in ancombc. Have alook at the github page: https://github.com/FrederickHuangLin/ANCOMBC