I tried to compare the different integration method on my data, and I found that scVIIntegration always produce the worse result. Then I run the script on https://github.com/satijalab/seurat/blob/HEAD/vignettes/seurat5_integration.Rmd, I found that the scVIIntegration result is still worse and different from the result from your vignettes, so could you help me to figure out what's wrong with my scVIIntegration?
Attached you can find my script and result.
test_different_integration_methods.zip
I tried to compare the different integration method on my data, and I found that scVIIntegration always produce the worse result. Then I run the script on https://github.com/satijalab/seurat/blob/HEAD/vignettes/seurat5_integration.Rmd, I found that the scVIIntegration result is still worse and different from the result from your vignettes, so could you help me to figure out what's wrong with my scVIIntegration?
Attached you can find my script and result.
test_different_integration_methods.zip