José Manuel

Hello. I have recently encountered the same problem. Re-running my analysis script changed the results. I also tried to re-run it in a different computer, and results were not consistent...

It is also mentioned at #8342 which is very similar of what I have observed.

Dear @saketkc, Thank you very much for your reply and sorry for the delay. I attach the same folder with the updated scripts. I labeled the old html notebooks as...

Sure, there you have it. I added the new files as filename_v5.0.2. [Seurat_reproducibility_issues.zip](https://github.com/satijalab/seurat/files/14478927/Seurat_reproducibility_issues.zip) Thank you very much for your time.

Dear @saketkc, Have you been able to reproduce the issues I encountered? Thank you.

Dear @saketkc, Sorry for the delay in my answer, but I have been out for holidays. Sure, I will send you the rds objects for both the test I am...

Dear @saketkc, Have you received our email? Please, confirm you got access to our data to resend it if you have encountered any problem. Best regards, JM.

Dear @saketkc, I would like to make you know that we have repeated the analysis but using the standard normalization pipeline instead of SCTransform, and all the reproducibility issues have...

Hi @Gesmira, FYI, I have disussed this already with @saketkc in this issue: #8501 We even exchanged additional information through emails. Unfortunately, we couldn't solve the problem. I suggest to...