Humann_renorm_table: sum>1


I used the humann_renorm_table function using humann3.5 and noticed that for both “relab” and “cpm” units the sum of is >1 and >1million, respectively. Should this cause concern?
I will also note that I did included the special features (unmapped, unintegrated and ungrouped).

Example for path abundance normalization:

humann_renorm_table --input 44WMGS_pathabundance.tsv --output 44WMGS_pathabundance_relab.tsv --units relab --mode community --special y --update-snames

44WMGS_pathabundance_relab.tsv (503.5 KB)

Thank you

The community totals for a freshly renorm’ed sample should always sum to 1 (or 1e6 in CPM units). The same is true for stratified gene families and gene family-like groups that you computed using the regroup utility (KOs, ECs, etc.). However, stratified pathway abundances are not guaranteed to sum to 1. This is because the pathway totals are not a linear combination of the pathway stratifications. Hence, while we force the pathway totals to sum to 1, and while we normalize the pathway stratifications against the unnormalized sum of pathway totals, this does not force the pathway stratifications to sum to 1.