Hi,

Hope someone may be able to point me in the right direction!

I've generated some polygenic risk scores for schizophrenia in a cohort of individuals with borderline intellectual disability. Trying to figure out a way to validate the scores I'm getting out of PRSice. Is there a way to do this?

My current results (with --all-score) look something like this:
https://ibb.co/jv9YQP5
(sorry couldn't place the table here in an easily legible format)

There are some patterns in my results, with some individuals having identical scores at particular p-values (is this just due to the stats involved in generating the scores?), and the scores are pretty low (clustering around 0) with some changing from positive to negative depending on p-value threshold. Is this typical of polygenic risk scores?

I've followed Marees et al 2018 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6001694/) and Sam Choi's tutorail (https://choishingwan.github.io/PRS-Tutorial/) to generate this, but I'm thinking I may have made errors somewhere along the line and would like to check my results somehow!

Any advice would be much appreciated!
Your sample size is simply too small. That will usually not give you any reasonable result. I suspect that as you've less than 100 samples, the clumping LD varies quite a lot, lead to more variants being removed than normally would (which lead to the small variant count). One way to get around that will be to use a reference panel (e.g. 1000 genome) which has a larger sample size. Though at the end of the day, with only 100 samples, I don't expect you to get any meaningful results. 

Given there are only 265 variants after clumping, it is very possible that you'd only have one or two SNP included in a particular threshold, which can then lead to the identical PRS. So I am not too surprise about your results. 
