runMagic problem too large

[Jing He]

Hi I am using runMagic to get gene activity for ~100 genes across ~60k cells, and it ran into memory issue. I am wondering if there is any way to resolve this?

==========================
Error in A %*% A: Cholmod error 'problem too large' at file ../Core/cholmod_sparse.c, line 92
Traceback:

1. runMagic(obj = x.sp, input.mat = "gmat", step.size = 3)
2. A %*% A
3. A %*% A
   ==========================

Thanks!
Jing

[chemistmarsy]

Hi Jing,

Please read this post:

#105

This method fixed my same issue with large dataset.

Best,
Ziyuan