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Problems interpreting and using reslults from smartPCA from Eigensoft

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,

snp gwas pca
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updated by Devon Ryan Devon Ryan • written by Ripeapple • Ripeapple

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.

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written by karl.stamm karl.stamm

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,

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written by Ripeapple • Ripeapple

Did you get this resolved? @Ripeapple Tks.

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written by Molly_K Molly_K

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