Saige GWAS giving p value/se == 0 for top hits

Hello,   I am running saige gwas and curating the results together and found that some of the top hits which we observed to be significant based on previous runs gave results as 0 for P & standard error. Has anyone faced or observed this error before? It would be great if someone can help me resolve this. [Image: image] Regards Akhil

Comments

5 comments

  • Comment author
    Ondrej Klempir DNAnexus Team

    See the following github thread, https://github.com/weizhouUMICH/SAIGE/issues/117. If I am not mistaken, it is likely that the values are of are high-impact on the trait, so the resulting pval is close to 0.

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  • Thank you so much for the response. I also got a standard error as zero too, how should I interpret that?

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  • Comment author
    Ondrej Klempir DNAnexus Team

    SE is also mentioned in the github thread above. I think that pval 0 and SE 0 relate to significant hits. I saw your question to SAIGE team, so they will likely know more.

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  • Got it I will wait for their response. Thank you.

     

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  • Here's an update: I haven't received a response from the developers yet. However, I have attempted to run the fastgwa algorithm using the dataset, and the results have been consistent.

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