However, the existing QC and filtering already performed doesn't preclude any additional custom filtering/QC that you may want to perform that will probably depend on your research question
Thank you very much for the prompt response. If I understand correctly, the metabolomics profiles are similar, excluding the quality control steps that are specific to the research question, is that right?
Additionally, I am also seeking to obtain the raw proteomics values for a specific set of proteins. I have noticed that all the values are in NPX format. Do you happen to have any suggestions on how to retrieve the raw values from NPX?
Personally I'm not very familiar with the metabolomics data.
I believe that only NPX data will be released. However, there is only minimal pre-processing between the raw NGS counts and the NPX values, where the data was background corrected according to the preprint description - normalized to correct for background and then adjust to control for within and across batch effects.
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Here is recently shared info about Olink data: https://community.dnanexus.com/s/question/0D582000000jnRACAY/new-data-release-on-ukbrap-olink-proteomics-data
Data documentation is then available here: https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=1839, see the Resources tab
This preprint details (in the supplementary material) the QC that was performed on the data: https://www.biorxiv.org/content/10.1101/2022.06.17.496443v1.full.pdf
However, the existing QC and filtering already performed doesn't preclude any additional custom filtering/QC that you may want to perform that will probably depend on your research question
Thank you very much for the prompt response. If I understand correctly, the metabolomics profiles are similar, excluding the quality control steps that are specific to the research question, is that right?
Additionally, I am also seeking to obtain the raw proteomics values for a specific set of proteins. I have noticed that all the values are in NPX format. Do you happen to have any suggestions on how to retrieve the raw values from NPX?
Personally I'm not very familiar with the metabolomics data.
I believe that only NPX data will be released. However, there is only minimal pre-processing between the raw NGS counts and the NPX values, where the data was background corrected according to the preprint description - normalized to correct for background and then adjust to control for within and across batch effects.
It is not possible to retrieve the raw values from the NPX values, and there is no intention to release the raw values in the forseeable future.
Thank you so much for the update.
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