Normalizing the merge abundance table


I have like 500 samples that I processed individually with metaphlan 3.0. Now I want to merge them all together with function. I am wondering if the merged table will have normalized abundance across all the samples? I want to compare those samples so want to make sure these are normalized.

I would really appreciate the clarification. Thanks in advance

What sort of normalization are you referring to? By default, metaphlan results are “relative abundance,” (0-100) so they’re normalized to the (within-taxonomic-level) total. That is, if you took the sum of everything at the genus level + the unclassified, it would be 100. This is a within-sample normalization though, and should not depend on other samples that you’re merging into a table.

Ok thank you. I guess then it should be fine.