Garnett Use Case Questions

[Olaf Baumeister Warren Holmes Corning]

Hi, 

I have a few questions about the use cases for Garnett:

* What is the minimum cell sample size?

* Can you still get meaningful data out of ambiguous markers?

* Can you use Garnett to divide a cell population on expression of only 2 genes (expression of X and Y, expression of only X, expression of only Y, expression of neither)? It would be convenient to have Garnett set the threshold between low and high expression.

Best,

Olaf

[hpl...@gmail.com]

Hi, The default minimum number of cells per cell type to be included is 8, you can modify the parameter min_observations in train_cell_classifier if you want to raise or lower the requirement. In practice, more cell examples will generate a more robust classifier.  I believe I answered your other questions in the previous post. 

Best,
Hannah