Danko-Lab
Running Error using "run.Ted"
Hello!
Thanks for your excellent work! But I met a running error when using function "run.Ted" to annotate the cell type of spatial spot referring to the well-defined scRNA-seq data. The single cell dataset includes 25002 cells and 16247 genes and there are 1752 spots and 18056 genes in the spatial transcriptomic data. The error occurred no matter I use the whole spots or 100 spot randomly chosen.
Below is the screenshot.
Really need your help, thanks a lot!!!
Thank you for your interest in our method.
This is mostly likely due to a memory issue. We are currently working on a version with improved memory usage, which is expected to be complete in 1-2 weeks. In the meantime, you may try decreasing the number of cores.
Let me know if it works for you.
Best,
Tinyi
On Mon, May 2, 2022 at 9:24 PM longmin0706 @.***> wrote:
Hello!
Thanks for your excellent work! But I met a running error when using function "run.Ted" to annotate the cell type of spatial spot referring to the well-defined scRNA-seq data. The single cell dataset includes 25002 cells and 16247 genes and there are 1752 spots and 18056 genes in the spatial transcriptomic data. The error occurred no matter I use the whole spots or 100 spot randomly chosen.
Below is the screenshot. [image: image] https://user-images.githubusercontent.com/70897310/166404443-eadd2cf8-4cec-45bd-add5-6316602953dd.png
Really need your help, thanks a lot!!!
— Reply to this email directly, view it on GitHub https://github.com/Danko-Lab/TED/issues/20, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4NHS2XCSIMEZRX5XVOJULVICS6JANCNFSM5U52DJKA . You are receiving this because you are subscribed to this thread.Message ID: @.***>
Dear user,
I have updated the current git repository to v1.4. This version has addressed the memory issue. You may try this and let me know if there it helps.
Best,
Tinyi