Small eigenvalues with polygenic() and large effB

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SBD
Posts: 1
Joined: Wed Nov 05, 2014 12:40 pm

Small eigenvalues with polygenic() and large effB

Postby SBD » Wed Nov 05, 2014 12:49 pm

Hi everybody,

I run a GWAS with pig data genotyped with the 60k Chip. For association analysis I first calculate pgresidualy using polygenic() and gkin (w="freq"). Than I use this as the new phenotype performing the GWAS. But when I look at the residuals, they are extremly small (E-5...). How does that can happen?
When I take a look at the outcome of my GWAS, the effB values are extremly high and can not be interpreted. Is their a connection between extremly low residuals and extremly high effB values? How can this be explained?

Thank you for any suggestion!

Sarah

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