I have tried a stratified analysis in PLINK using Cochran-Mantel-Haenszel test for IxJxK tables and specifying the three phenotypes in a cluster file but I get "-9" as the p-value for all the SNPs tested. Any other idea?
I suggest you have a look at the following papers:
- Across-line SNP association study of innate and adaptive immune response in laying hens;
- Across-line SNP association study for direct and associative effects on feather damage in laying hens;
The SNP effect is modeled so to capture those effects that are common across populations (i.e. in all populations).
Hope this helps,
Filippo
maybe try meta-analysis or association test adjusting for co-variate, such as PCs
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