at file ../Core/cholmod_dense.c, line 102 about scgsva HOT 4 OPEN

Hi @zznx,
I think you may have an extremely sparse matrix which means you had too much zeros in you data. You can do some trimming which may help you. Or you can run your analysis on a lager machine which may have enough memory. Hopes this will help
Kai

from scgsva.

When I run the code,it finally works!

Seurat.object=subset(x = Seurat.object, features = VariableFeatures(object = Seurat.object)
library(scGSVA)
hsko<-buildAnnot(species="human",keytype="SYMBOL",anntype="KEGG")
res<-scgsva(pbmcs,hsko)

I think there might be something wrong, and when I run the code I get an error

library(scGSVA)
Seurat.object=subset(x = Seurat.object, features = VariableFeatures(object = Seurat.object)
Error in `[[<-`(`*tmp*`, dimreduc, value = tryCatch(expr = subset.DimReduc(x = x[[dimreduc]],  : 
  [[<- defined for objects of type "S4" only for subclasses of environment

from scgsva.

Hi @zznx,
I guess you may need to load the Seurat package before you do subsetting.
Kai

from scgsva.

Hi @guokai8
I have loaded the Seurat package but I still have the above problem.
Jx

from scgsva.