choishingwan / PRSice

A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores
http://prsice.info
GNU General Public License v3.0
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No error but getting no results #331

Closed sakuramodokich closed 1 year ago

sakuramodokich commented 1 year ago

Hi, PRSice.log I ran PRSice but the barplot show zero p-values and grey bars, and no significant results were generated. Attached is the log file.

sakuramodokich commented 1 year ago

PRSice_BARPLOT_2023-07-15 PRSice_HIGH-RES_PLOT_2023-07-15

sakuramodokich commented 1 year ago

@choishingwan Is this ordinary? Please kindly advise on a solution.

JoniColeman commented 1 year ago

If you check the .prsice file, I imagine you will find that the polygenic risk scores are all extremely significantly associated with the phenotype, such that all the p values are lower than machine tolerance (and hence set to 0).

I suspect this is due to overfitting – is there sample overlap between your target cohort and your base GWAS?

choishingwan commented 1 year ago

Thanks @JoniColeman!