Question: GWAS missing p-values
1
gravatar for emmacomp
5 months ago by
emmacomp10
emmacomp10 wrote:

Hello, when running a logistic regression on 250 cases and 2000 controls, the resulting GWAS has completely missing p-values in the middle. I have attached the histogram of -log(p) values, where you can see the missing values in the middle. Has anyone run into this problem before?

enter image description here

ADD COMMENTlink modified 5 months ago by zx87547.7k • written 5 months ago by emmacomp10
1

QQ plots and Manhattan plots would be more informative. See qqman for plots.

ADD REPLYlink written 5 months ago by zx87547.7k
1

One requires a Google account to see your figure, whose link is not appearing in your question (please edit your question's text). You have neither given the commands that you have used, nor have you mentioned the program; so, we can only really speculate about the issue. NAs may be returned if, for example, a particular SNP is only genotyped in a couple (or just a single) sample. I note that your cohort is imbalanced, too.

ADD REPLYlink written 5 months ago by Kevin Blighe45k

Before it became invisible, it was just a histogram of logged pvalues, with extremes on the left and the right handside, middle pretty much blank.

ADD REPLYlink written 5 months ago by zx87547.7k
1

emmacomp : How to add images to a Biostars post

ADD REPLYlink written 5 months ago by genomax69k
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