-
Notifications
You must be signed in to change notification settings - Fork 6
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Any way to speed up the calculation? #8
Comments
Thanks for using our tool! The reason why ENIGNA trace norm need to perform SVD for each CSE in each round of gradient calculation. Therefore it takes time to optimise when apply ENIGMA trace norm on large datasets (>1000 samples or >5000 spots). Even though current version need to cost a long time on large dataset, it should not cost such long time (over 24 hrs) on ~500 samples. Here is my current thoughts to fix the issue:
The parallelized ENIGMA is under development and I would upload soon. Hope above information is helpful, and please let me know if you suppose have any new questions. Best, |
Hey Have you fixed your question, if you still have problem, could share the data with me (omit some important information) and I could help you to address Best, |
Hi,
I've tried to run Enigma trace norm for ~500 TCGA samples using my own scRNA data (15 cell types with ~ 10000 genes) as the reference (in the aggregated 10000x15 matrix but not the Seurat object). It has been running over 24 hrs. I wonder if there is any tip to speed up the calculation or if it is possible to make a multi-core version?
Thanks,
YC
The text was updated successfully, but these errors were encountered: