cell type assignment with negative expression

[goterm]

Hi,

is there a way to define a signature with negative expression (or low expression) of a specific marker?
For instance CD27-IgD+ and CD27+IgD+ cells?

How would the signature vector would look like?

thank you

[wtwt5237]

Hi @goterm

You can just invert the expression of that particular negative marker gene in your original expression matrix (so it becomes a positive marker gene), and you can then just use SCINA as usual. Hope this is helpful

Thanks!

Tao