The problem when using a large scRNA data

[youwh1996]

[youwh1996]

Dear When I use this package to analyze the scRNA data with over 20000 cells， the package cannot run because of the dataframe expression was too large? Could you please address this bug?

[millersan]

Could you show your code? I can run in more than 20000 cells.

[youwh1996]

Could you show your code? I can run in more than 20000 cells.

I used the CreateObject_fromSeurat function to run my data. However, This step failed because the dgmatrix was too large to convert to expression dataframe.

[hzaumsq]

I also meet the same problem! 100000 cells test <-CreateObject_fromSeurat(Seurat.object=data,slot="counts",cell_type="immune_annotation",data_source="UMI",scale.factor = 10^6,Org = "Homo sapiens") Error in asMethod(object) : Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 102

[hzaumsq]

@millersan @youwh1996 @ShellyCoder

[millersan]

I can run in 78000 cells.

[hzaumsq]

I can run in 78000 cells.

I still can't run in 100k Cells @ShellyCoder @

[AdelynTsai]

I have about 140K cells and also has been stuck at TransCommuProfile