at file ../Core/cholmod_dense.c, line 102

[zznx]

Hi @guokai8

Error in asMethod(object) : Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 102

Thank you for the package.And how to fix it

[guokai8]

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

[zznx]

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

[guokai8]

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

[zznx]

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