Closed aritra90 closed 2 years ago
Hi @aritra90,
Sorry for my late reply. This is because by default, SPA only applies to markers with p-value (under the normal approximation) < 0.05.
We have just released a new version 1.0.0. It has computational efficiency improvements for both Step 1 and Step 2 for single-variant and set-based tests. We have created a new program github page https://github.com/saigegit/SAIGE with the documentation provided https://saigegit.github.io/SAIGE-doc/
The program will be maintained by multiple SAIGE developers there. Please feel free to try the version 1.0.0 and report issues if any.
Thanks! Wei
Hi,
I am running single-variant association tests using SAIGE and getting same values for the pvalue and pvalue.na (with and without SPA) fields. I was wondering when would this happen and is it a common phenomenon or am I missing something?
Thanks