SeuratToExpressionSet about bisque

[brandonjew]

Hi @chenx9,

Thanks for your interest in our method! I believe that error arises when the expression data in the seurat object is too large. The object is fine before the conversion since it's stored as a sparse matrix, but it is converted to a dense matrix by this function. As far as I can tell, the ExpressionSet object does not support sparse matrices. Unfortunately, this would require editing the Biobase:::ExpressionSet source code or finding a machine with more memory. Please let me know if you have any other questions.

Thanks,
Brandon

[chenx9]

Thanks for your reply.
I tried the Biobase:::ExpressionSet function and got a similar error.
Does that mean I can't use it to process large data sets?

Thanks

[brandonjew]

That's correct, someone would have to edit the ExpressionSet source code to use sparse matrices. Tools like CIBERSORTx have a web server that will handle the computation on their side if you're comfortable uploading the data.