Question: PLINK meta-analysis when there is SNP for just one study
0
gravatar for rkl
3 months ago by
rkl0
rkl0 wrote:

Hi,

I am encountering an issue with my meta-analysis. Although, plink reads all 3 studies, when there is 1 study it outputs NA for the betas, SEs and associated values even though I specify for it to report all

--meta-analysis SP_reformatted.assoc GC_reformatted.assoc AP_reformatted.assoc + qt report-all

Would really appreciate advice

Thanks

plink • 156 views
ADD COMMENTlink modified 3 months ago by zx87547.1k • written 3 months ago by rkl0
1

What plink build are you using? This should have been fixed in plink 1.9 in December 2017.

ADD REPLYlink written 3 months ago by chrchang5234.9k

I am guessing, if we do not use report-all, that SNP won't be present in the output file. With report-all option we are saying list the SNP even if there is no stat, hence NA.

I prefer METAL for meta analysis, which reports for all SNPs even if that SNP only present in one study.

ADD REPLYlink modified 3 months ago • written 3 months ago by zx87547.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1987 users visited in the last hour