Problem with training my dataset - only few cells got trained into limited cell types

[thao....@gmail.com]

Hi,

I have markers for 20 cell types (5 markers per cell type). When I train the classifiers (using train_cell_classifier), only 3 out of 20 cell types were trained. I have more than 6000 cells in total, and less than 20 cells were trained into each of the 3 groups + unknown (500). What did I do wrong?

Also, for the expression data, should I use raw counts to start with? or normalized counts?

Thanks!

[Hannah A Pliner]

Generally when cells aren't chosen for the training set it indicates that the markers aren't expressed in enough cells. Have you checked that the markers you provided are expressed at an appreciable level in your dataset? I also recommend using the check_markers function to determine whether any of your markers are highly ambiguous.

You should use raw counts, Garnett will do the normalizing for you.

Best,

Hannah Pliner, Ph.D.

Lead Data Scientist for Single Cell Genomics

Brotman Baty Institute for Precision Medicine

Seattle, WA

hpl...@uw.edu

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