Closed oalavijeh closed 2 years ago
Hi @oalavijeh,
Which version of SAIGE are you using?
Thanks, Wei
Dear Wei,
We are using SAIGE-GENE v0.42.1
Many thanks
Omid
Hi Omid,
Sorry for my late reply.
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
Dear Wei,
Thank you such an amazing tool! I was trying to run SAIGE on a quantitative trait and when running SPA_test step2 I keep getting an error:
"Error in scoreTest_SAIGE_quantitativeTrait_sparseSigma(G0, obj.model.sub$obj.noK, : objest "isSparse' not found Execution halted
I have tried setting "isSparse" to TRUE,FALSE and just deleting it but this does not work.
I am working in an airlock using biobank data so cannot easily share code I am afraid but can offer screenshots if needed.
Many thanks for your help