cellassign
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Size factor of CellAssign
Directly compute size factor by sum of each cell's expression( through adata.obs["size_factor"] = adata.X.sum(1)
) will lead to wrong celltype assignemnt when I recently run cellassign example by scvi-tools https://docs.scvi-tools.org/en/stable/user_guide/notebooks/cellassign_tutorial.html. The dataset tutorial used have a size factor in its meta data and I do not know how it comes from, there also a method to compute size factor in tutorial by sum of a cell's all expression but when I compute by this method, Cellassign just can not get right way to assign celltype,it's totally wrong result:
Using size factor which is tutorial dataset offered
After computing size factor by adata.obs["size_factor"] = adata.X.sum(1)
So, I have two questions: 1) what is exactly size factor is and its function which I tried to find something on Google but little information can get. 2)why size factor impact results so much and what is your suggest. Looking forward your relay. Best wishes!