I am looking for NMR metabolites in UKB RAP phenotypes. I have a few questions:
1.) May I know how many NMR metabolites are in UKB RAP?
2.) Can you help how to find all metabolites?
3.) What QC steps generally were followed?
Thank you, I see and have access to that id 220. I used all the field ids present in 220. I did the extraction from the database and only found some of the metabolites present in 220. Thank you, I will check into the column again and I will get back to you.
Thank you so much for the help. I could able to get the metabolites. Do we have any QC steps that need to be followed before doing the analysis? or can we use the metabolites as it is?
Comments
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For NMR metabolites, you may consult this UKB page:
https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=220
See Tabs:
A) Data fields - contains all the NMR metabolomics data fields + details, e.g. histogram (example - https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=23440).
B) Resources - contains useful information such as distribution of biomarker values and QC.
https://biobank.ndph.ox.ac.uk/showcase/ukb/docs/nmrm_companion_doc.pdf
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If you have access to these fields, you should be able to also find those in Cohort Browser.
In addition, there is a recent webinar on Metabolomic data:
https://www.youtube.com/watch?v=kBSHDjYJYG0 (30:35)
Thank you, I see and have access to that id 220. I used all the field ids present in 220. I did the extraction from the database and only found some of the metabolites present in 220. Thank you, I will check into the column again and I will get back to you.
Thank you so much for the help. I could able to get the metabolites. Do we have any QC steps that need to be followed before doing the analysis? or can we use the metabolites as it is?
I believe we can use it as it is. Data was qced already on the UKB side (see the doc I shared last time).
You can read this article, presenting a real analysis:
https://www.medrxiv.org/content/10.1101/2022.06.12.22276286v1.full.pdf
Check the results, statistical methods and also section Data sources.
Thank you so much for the response. I believe i have seen this paper. Thank you for sending the paper again.
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