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guokai8 / scGSVA

scGSVA: Perform GSVA for single cell RNA seq
GNU General Public License v3.0
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Memory issue #12

Open Cristinacondel1 opened 1 year ago

Cristinacondel1 commented 1 year ago

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!

guokai8 commented 1 year ago

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

guokai8 commented 9 months ago

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