NaNs during `SelectGenes()` about liger HOT 1 CLOSED

Hi Shani,

Thanks for reporting this. From what I know so far, a negative value given to functions like sqrt() or log() causes an NaN. So back to the specific step as shown in your warning message. I would need some exploration in order to debug it.

• gene_expr_mean is a vector of mean values for each row of the [email protected][[i]]. Can you check if any negative values came from here? e.g. any(rowMeans([email protected][[1]]) < 0), where 1 is for your first dataset and you might want to do this to all datasets there.
• nolan_constant is calculated from [email protected][[i]], and is impossible to be negative unless the raw data is not a non-negative raw count matrix. Can you confirm about this?

If these are not the case, I'll need some more investigation then.

Best,
Yichen

from liger.