Problems interpreting and using reslults from smartPCA from Eigensoft

Question

[Ripeapple]

Hi, everyone,

I have been using smartPCA in Eigensoft software for computing PCAs on my SNPs. I got eigenvectors and eigenvalues as output. But I don't know how to interpret the log file and how to use these output files to control the population structure in GWAS.

Any input are appreciated!

Thanks a lot,

[karl.stamm]

Not knowing how to use a PCA result to control a GWAS is not related to smartPCA or Eigensoft specifically; You should familiarize yourself with PCA in general, and covariate adjustment in general; then if there's a problem with the technology we can discuss that separately. So there's three under-specified questions here, and we can't really solve everything in a forum post.

[Ripeapple]

Hi, Karl, I am sorry for the misinterpretation, I mean I didn't get the PC scores or loadings which I could use as covariates in my association tests, so I am wondering how can I use the output files? Thanks,

[Molly_K]

Did you get this resolved? @Ripeapple Tks.