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Variabel pvalues

Posted: Thu Sep 11, 2014 12:20 pm
by AlfredAlfred
Hi!

I am running VariABEL analyses. I want to do Manhattan plots on the pvalues for the variance for each SNP, but I dont know where I should get pvalues from?
First I used the "chisq" column, which I had transformed to p-vales (via pchisq). But these pvalues was far to low to be realistic for a SNP, so I guess that was wrong. Could anyone please help which column that I should use, and how to get pvalues?

Many thank
A