Post by carolina on Feb 5, 2016 9:34:02 GMT
Dear Yian... I have seen in many papers they exclude the cohort used to calculate LD (bfile in the file) from the meta-analysis but others then do not. Of course, I will prefer to keep all the cohorts in order not to compromise my power but not sure it is correct. Could you give me your opinion?.
In addition, I have in my meta-analysis some cohorts which are from admixed origin and have excluded them from the GCTA analysis as the LD is calculated in the CEU population, but from these cohorts some have less than 30% admixed individuals, and I am thinking perhaps I am being too stringent (particularly considering my tophits are quite common). As by doing so I lost 20% of the sample size in the meta-analysis and can not evaluate some of the loci GWS in the meta-analysis with all samples as they do not reach GWS in the only-CEU analysis.
In addition, I have in my meta-analysis some cohorts which are from admixed origin and have excluded them from the GCTA analysis as the LD is calculated in the CEU population, but from these cohorts some have less than 30% admixed individuals, and I am thinking perhaps I am being too stringent (particularly considering my tophits are quite common). As by doing so I lost 20% of the sample size in the meta-analysis and can not evaluate some of the loci GWS in the meta-analysis with all samples as they do not reach GWS in the only-CEU analysis.
