Is depthNorm in scGAD equivalent to BandNorm?

[LHXqwq]

Is 'depthNorm = TRUE' in the scGAD function equivalent to BandNorm? Should I first use BandNorm and then calculate the scGAD for each gene and perform 'depthNorm = TRUE', or should I directly use 'depthNorm = TRUE' in scGAD without using BandNorm?

[sshen82]

Hi,
The normalization in BandNorm is to eliminate the band bias among cells, and the normalization in scGAD is to eliminate the sequencing depth within gene regions for those cells. My experience is that doing BandNorm first can increase the performance, but not by a lot. If you have a huge amount of cells, you might ignore the step to save time.

Yours sincerely,
Siqi Shen