Hi there,
I ran ANCOM-BC2 multiple pairwise comparisons, and need help on interpreting my res_pair results, mainly to confirm the difference between diff_robust and passed_ss.
Below is my raw data as extracted from the res_pair file (filtered based on diff=TRUE), showing all diff, diff_robust and passed_ss:
I am quite confused because based on my understanding from R documentation , it says: "res_pair, a data.frame containing ANCOM-BC2 pairwise directional test result for the variable specified in group: columns started with diff: TRUE if the taxon is significant (has q less than alpha). columns started with passed_ss: TRUE if the taxon has passed the sensitivity analysis."
R documentation also indicates separately from the res_pair description that: "columns started with diff_robust: TRUE if the taxon is significant (has q less than alpha) and robust in the sensitivity analysis (passed_ss is TRUE)."
My understanding is that diff =TRUE is where q-value <0.05, and diff_robust further means it is significant after multiple testing correction AND sensitivity analysis. But how come my passed_ss for some is FALSE when diff_robust is TRUE? So I am quite confused now what is the exact difference between diff_robust and passed_ss?
I tried to understand further from the main tutorial under 5.6 ANCOM-BC2 multiple pairwise comparisons, it was stated that "in the subsequent heatmap, each cell represents a log fold-change (in natural log) value. Entries highlighted in green have successfully passed the sensitivity analysis for pseudo-count addition.", which when I looked into the tutorial code, the green entries were plotted based on diff_robust=TRUE.
Then in the published protocol, as referred to Figure 4, "Genera represented in black are significant without a multiple testing correction, whereas those highlighted in green are significant after multiple testing correction. Additionally, genera marked with an asterisk are also significant after applying the ANCOM-BC2 (SS filter)." - is it correct to imply that those highlighted in green are diff_robust = TRUE, those with asterisks are where passed_ss = TRUE too?
Can anyone enlighten me please how to interpret these properly?
Thank you so much!!
