Hey,
I didn’t see your new site, will definitely take a look.
I was running it on 2 different sets, ~400k snps x ~200 people each and got as the result all 0.
Then I processed those sets with snip-snip and run fastlmm again and it worked (on about 20k snps).
I don’t have many missing values, so it shouldn’t be a problem. Format was exactly the same for 400k and 20k. So it should be the size or I don’t know…
Thank you for your answer.
Katya