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WWXkenmo / ENIGMA

A fast and accurate deconvolution algorithm based on regularized matrix completion algorithm (ENIGMA)
MIT License
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get_cell_proportion taking forever to run #9

Closed ankur26197-acog closed 1 year ago

ankur26197-acog commented 1 year ago

Hi, I am running the code available here stepwise(except step 2 because my ref_type is single_cell). I am using same datasets as well. I have loaded reference in Seurat object. Running get_cell_proportion is taking forever. I wanted to ask if it did happened for you too. I am using RLR since the document says that CIBERSORT takes longer time.

Thank you.

WWXkenmo commented 1 year ago

Hey,

Have you run the batch_correct step, because when your ref_type is single cell, you need to run S-mode to get the reference profile matrix (n by k), in which k = number of cell types & n = number of samples. one way to perform quickly check is to look the dimension of object@ref, and you would see that without batch_correct step, the ref matrix is simply single cell gene expression matrix (n by m) m = number of cells. Which definitely take forever to run

Best, Ken

ankur26197-acog commented 1 year ago

Hi, Thanks for the reply. It worked after applying batch correction. However the document quotes When the ref_type = “single_cell”, ENIGMA would automatically use S-mode to correct batch effects.. My ref_type is single_cell so I wasn't explicitly doing it.

WWXkenmo commented 1 year ago

Hey,

Now I understand the where lead to the misunderstanding, I would fix this later

Best, Ken