Entering edit mode
5.3 years ago
emmacomp
▴
10
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?
QQ plots and Manhattan plots would be more informative. See qqman for plots.
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.
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.
emmacomp : How to add images to a Biostars post
Did you ever get past this error? I am having the same problem and was wondering what might be causing this?
The user never replied in order to better describe the problem. Perhaps you can describe your problem more? Better, please show all commands that you have run, and explain your input data, with small examples of this input data, please.