cholmod error 'problem too large' at file

[ncborcherding]

cholmod error 'problem too large' at file

[atimms]

I get the cholmod error, so I attempted your solution, but then got the error message:

expr_matrix <- cbl_dev_clean@assays$RNA@counts #sparsematrix
expr_matrix <- expr_matrix[tabulate(summary(expr_matrix)$i) != 0, , drop = FALSE] #remove any feature without a single count
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'i' in selecting a method for function '[': $ operator is invalid for atomic vectors

Any ideas?

Thanks for providing this tool.

Andrew

[ncborcherding]

Hey Andrew,

Sorry for the delay - I actually forgot to put in the nessecary library

library(Matrix) #Here is the problem
expr_matrix <- integrated@assays$RNA@counts #sparsematrix
expr_matrix <- expr_matrix[tabulate(summary(expr_matrix)$i) != 0, , drop = FALSE] #remove any feature without a single count
expr_matrix <- as.matrix(expr_matrix) #convert to matrix

Hopefully that helps, I did check the code with and without the library(Matrix) and I was able to reproduce the error you saw. So I am hoping that is all the fix, but please let me know if you have any other issues.

Thanks
Nick

[atimms]

Hello Nick,

Thanks for getting back to me.

That resolved the error message as you expected unfortunately my dataset still seems to big, so I get the same Cholmod when running the as.matrix step.

I guess 70k cells must be too many and I don't want to split my seurat object into different samples.

Andrew

[ncborcherding]

If any user is still having this problem - there is no longer a conversion from a sparse matrix to a full matrix - this eliminates the error (will be in the dev branch of escape committing this afternoon).