Problem too large

[YaobangWang]

Hi,
I'm glad that scATOMIC helped me a lot in distinguishing tumor from non-tumor cells.
However, when I ran a large dataset of 67000 cells, the following error occurred: "Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 105".
This large dataset is a combination of single-cell RNA sequencing data from 25 cancer patients. I wonder how I should do the right analysis in this situation? Plan A: I will divide this large dataset into 25 sub-datasets on a per-patient basis, and then analyze each sub-dataset individually. Plan B: I will split these 67,000 cells into two equal parts at a 1:1 ratio, and then analyze each part separately. Which of the above two plans is the better choice? I would be very grateful, if you have any suggestion to solve this problem!

[Ido Nofech-Mozes]

Hi Yaobang,

Thank you for your interest in scATOMIC!
scATOMIC is designed and has assumptions built into the methods that there is only one tumour sample when it is run.
So I definitely recommend trying Plan A for annotation, followed by merging all the annotation results.
Please see issue #21 for some more details.

Best,
Ido