PlateID to sample id linker for proteomics data?
Hello,
I am currently attempting to replicate the analysis conducted in the human proteome paper (Bioarxiv 2022) using a smaller sample size to validate my GWAS results, which were run on the same dataset using Saige. However, upon initial comparison, I noticed differences in the Manhattan plots. Specifically, I observed that several top hits on chromosome 5 were missing when I performed a similar analysis using Saige.
Upon further examination of the paper, I discovered that there were some changes in the covariates used in the GWAS analysis. As a result, I would like to extract all the covariates utilized in the paper in order to replicate this specific portion of the analysis quickly.
During my investigation, I also came across plate IDs and dates, but I am unsure how to link them with the sample IDs present in the dataset. I would greatly appreciate your assistance in providing the linker file and any other necessary information required for the analysis.
Thank you for dedicating your time to address this matter, and I eagerly await a solution.
Best regards,
Akhil
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3 comments
Any comments or responses would be appreciated?
I'm not sure if this data exists for the case proteomics samples, but its available for the control samples: https://biobank.ndph.ox.ac.uk/showcase/rectab.cgi?id=1071
Perhaps you can try reaching out to the authors to learn more how they performed their analysis and if that data is supplied on the UKB-RAP.
Resource 4654 in the proteomics category lists the table relations in the Olink data: https://biobank.ndph.ox.ac.uk/showcase/refer.cgi?id=4654.
They will need to use the Showcase field for plate ID (F30901) to link to the resource datasets by plate ID, plus join to the assays via encoding 143. The encoding lookup provides the link between the olink_data protein_id and the Assay in the resource datasets.
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