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dnanexus / UKB_RAP

Access share reviewed code & Jupyter Notebooks for use on the UK Biobank (UKBB) Research Application Platform. Includes resources from DNAnexus webinars, online trainings and workshops.
MIT License
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change threshold of fold change from 0.1 to 1.1 #30

Closed dryezl closed 1 month ago

dryezl commented 11 months ago

change threshold of fold change from 0.1 to 1.1, as described in Figure 1 of https://doi.org/10.1093/braincomms/fcac155. "Proteins with a P < 0.05 and fold-change >10% are displayed".

Arkarachai commented 7 months ago

Thanks @dryezl Our scientist who takes care of this project is on the leave and will return in March next year. We will address this upon the return.

Arkarachai commented 7 months ago

@ajlee21

ajlee21 commented 1 month ago

Thank you for your suggestion. It does look like we are using the same criteria for DEG de_protein_df <- results_df[results_df[,'P.Value']<threshold & abs(results_df[,'FC'])>0.1,] as mentioned in Figure 1.

In general, this notebook was meant to demonstrate performing protein DE analysis on the UKB-RAP and not meant to perform a rigorous recapitulation of the publication perse.