Question: Specifying sample size from GWAS summary statistics for meta-analysis
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gravatar for helen
7 months ago by
helen40
helen40 wrote:

The meta-analysis tool I am using (METAL) requires users to specify Weight (sample size) from each GWAS summary statistics file. I have a sumstat file contains columns Nca, Nco, and Neff, but the Neff does not equal to the value of Nca + Nco. I was wondering what the sample size means here? Should I create a new column "N" to combine Nca + Nco? Thank you in advance!

snp • 350 views
ADD COMMENTlink modified 7 months ago by Sam3.3k • written 7 months ago by helen40
1
gravatar for Sam
7 months ago by
Sam3.3k
New York
Sam3.3k wrote:

Neff is the effective sample size, you can read more here and here. You can use that as your weight column for METAL if I remember correctly.

ADD COMMENTlink written 7 months ago by Sam3.3k

Thank you, Sam. Then what if I have another sumstat that doesn't have any information regarding the sample size. Would you recommend me to calculate the effective sample size from the raw sample size mentioned in the original paper and transform it using the statistic methods like in the linked articles?

ADD REPLYlink written 7 months ago by helen40

Do you have the SE or the case control sample size? You can calculate the effective sample size from the number of cases and control, or you can use the SE for the meta analysis.

ADD REPLYlink written 7 months ago by Sam3.3k
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