Hi,
I am conducting a GWAS Meta-analysis, and while conducting QC, some of the cohorts I am including have shown a discrepancy between the reported SAIGE P value, and the P value calculated from Z statistic. (Please see attached plot for pattern, showing -log10P for observed P value vs -log10 of P value calculated from Z statistic)
We were wondering what could be the cause of this discrepancy.
Hi, I am conducting a GWAS Meta-analysis, and while conducting QC, some of the cohorts I am including have shown a discrepancy between the reported SAIGE P value, and the P value calculated from Z statistic. (Please see attached plot for pattern, showing -log10P for observed P value vs -log10 of P value calculated from Z statistic) We were wondering what could be the cause of this discrepancy.
Thank you!