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stefpeschel / NetCoMi

Network construction, analysis, and comparison for microbial compositional data
GNU General Public License v3.0
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Aitchison or Bray #32

Closed AndreaQ7 closed 2 years ago

AndreaQ7 commented 2 years ago

Hello everyone,

I have a doubt about the correct approach to use for my data: I have performed shotgun metagenomic and classification using Kraken2/Bracken, than I have imported Bracken genera table into a phyloseq object. The otu table of this object have been already transformed to relative abundance (thus it not contains raw counts), is it right to use Aitchison distance in this case to create construct the network in the function "netConstruct"? thank you in advance for your help

stefpeschel commented 2 years ago

Hey,

Sequencing data are generally compositional, regardless of whether they have been transformed into relative abundances or not. This is described in more detail in our manuscript. I would recommend using the Aitchison distance for your data since it's an appropriate dissimilarity measure for compositional data.

Best, Stefanie

AndreaQ7 commented 2 years ago

Thanks a lot Stefanie for this confirmation BW