Saket Choudhary

Hi @jmgs7, thanks for providing the scripts. Can you rerun them outputting your `sessionInfo()` at the end?

Hi @jmgs7, can you also additionally output: ```r sessionInfo() RNGkind() ``` Thanks!

Hi @jmgs7, thanks for sharing the sessioninfo. Can you install latest Seurat (v5.0.2) and share the files again? I have not been able to reproduce this at my end yet.

Unfortunately no. Can you confirm if you notice the same issue without 'vars.to.regress'

hi @jmgs7, would you be able to share the objects with me post you run SCTransform? You can save it just after the SCTransform step.

Hi @jmgs7, thanks for sharing the objects. Can you also share the objects you get without invoking `vars.to.regress`. It seems the residuals are slightly different between the objects (but I...

Thanks for the reproducible example @nyanmo. I can confirm this is currently a bug that I should be able to fix soon. Also related https://github.com/satijalab/seurat/issues/8148#issuecomment-1910297805

Hi @genome2020, Can you update your Seurat to latest version (5.0.3) and try again? Your current version is `Seurat_4.9.9.9067`.

Thanks everyone for your patience. https://github.com/satijalab/seurat/commit/e5171f7a6b2b1145753b0b1606d16e30d6b0984d should speed up `PrepSCTFindMarkers` by default (and also supports parallelization - though that might not always lead to speedups given the data splitting being...

You can try the RPCA based integration as [suggested in this vignette](https://satijalab.org/seurat/articles/integration_large_datasets.html).