I'm doing a GWAS using shared controls for 2 diseases, and I need to check if there is any statistical relation between the controls. I'm doing the 1-d.f. Mantel-extension test for differences in allele frequencies of SNPs between subjects, and I'm not really sure abut the results of the test. Which p-value is a "good" one on this kind of test for ensuring that there is no relation between the controls? Thanks in advance.
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bloodyangel.minus2 •
I think you are looking for this publications:
First paragraph from their discussion:
In this manuscript, we describe methods for combining and adjusting P-values in the context of the shared controls design. We suggest that P-value based analysis provides powerful means of inference for association studies that reuse control individuals.
Hope that helps.
I had read that publication, however it doesn't have a reference value for checking the relation between controls. Thanks, though.
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May I know how to do Mantel-extension test for differences in allele frequencies of SNPs?
I have read some materials but I am still very confused about how to prepare the data and which variable correspond to which one?
I am too desperate to ask here.........
Thanks
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