search

ShellyCoder / cellcall

inferring cell-cell communication from scRNA-seq of ligand-receptor
73 stars 20 forks source link

The problem when using a large scRNA data #9

Open youwh1996 opened 2 years ago

youwh1996 commented 2 years ago

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 commented 2 years ago

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

youwh1996 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

@millersan @youwh1996 @ShellyCoder

millersan commented 2 years ago

I can run in 78000 cells.

hzaumsq commented 2 years ago

I can run in 78000 cells.

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

AdelynTsai commented 1 year ago

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