enhance gene expression of enhanced clusters taking too long to run

[joachimsiaw]

Hi. Thank you for the wonderful tool you have developed. I was trying to generate enhanced gene expression profile for my enhanced spatial clusters. I wanted to run the enhanced gene expression algorithm on about 14000 genes. This process was running for almost 2 weeks until i stopped it.
I ran this with slurm using 100 cores.
Do you have any suggestion on how i can speed up this process?? Or is this expected for the number of genes i wanted to analyze?

Thank you

[edward130603]

Hi there. A couple of solutions.

1. Try using a smaller number of genes that you are interested in.
2. Use the lm method instead of xgboost.
3. Set the nrounds parameter for xgboost.

FYI @senbaikang, if you have time in the future, this is another function that can be parallelized for great performance increases.

[senbaikang]

Sure, I will have a look when I get free.