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weizhouUMICH / SAIGE

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Same values in pvalue and pvalue.na fields #376

Closed aritra90 closed 2 years ago

aritra90 commented 2 years ago

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

weizhouUMICH commented 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