Clarification on technical-variation adjustment for NMR metabolomics Phase 1 + 2 data

Yazhou Chen

I am planning to analyse the NMR metabolomics Phase 1 + Phase 2 dataset in my approved UKB project.

In the NMR metabolomics companion document (Phase 2 update), the section “Recommended approaches for data preprocessing and analysis” cites Ritchie et al. (Sci Data 2023, doi: 10.1038/s41597-023-01949-y ) as a “detailed report on quality control and removal of technical variation”.

Could you please confirm:

  1. Have the concentrations released in the UKB Data Showcase / RAP already been processed with the full pipeline described by Ritchie et al. ?
  2. Or are the values currently provided only processed through the standard Nightingale + UKB QC pipeline—which is generally sufficient for analysis without further preprocessing—while researchers may still choose to apply the extra adjustment themselves (e.g., using the ukbnmr R package from Ritchie et al.) for additional refinement?

Knowing this will determine whether I need to perform that preprocessing step locally before downstream analyses.

Thank you very much for your help.

Comments

1 comment

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  • Comment author
    Melissa L The helpers that keep the community running smoothly. UKB Community team Data Analyst

    Dear Yazhou, 

    Thank you for your query, 

    The NMR metabolomics data available on the UKB-RAP has not been processed using the ukbnmr R package described in Ritchie et al. 

    Best Wishes

    Melissa 

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