Memory issue

Open Cristinacondel1 opened this issue 2 years ago • 2 comments

Hi!

I'm trying to run the function on 100756 cells for the GO genesets and I'm always running into the same memory issue:

In asMethod(object) : sparse->dense coercion: allocating vector of size 17.8 GiB

I'm doing this on a cluster with quite a big capacity so I decided to fraction the cells to be able to run it. I was wondering if then the data from different runs would be comparable, because from what I understand from normal GSVA the results are only comparable intradataset.

Thank you!

May 12 '23 07:05 Cristinacondel1

Hi @Cristinacondel1 , Yes. You are correct. It could be only comparable within the same data. I am working on the memory issues and will update the function in next version. Best, K

Jun 21 '23 04:06 guokai8

Hi @Cristinacondel1 , Please try the new version by setting the batch parameter within the scgsva. K

Nov 28 '23 22:11 guokai8