Gene expression normalization

Question

Gene expression normalization

Closed this issue a year ago · 2 comments

Hi, I want to use the tool with scRNAseq data. Is normalization needed? Or is UMI fine?

Answer 1 · 2023-03-15T02:02:22.000Z

Hi!

It depends on the aggregation method you use for summarizing the expression within a cluster. If you are using an aggregation of the fraction of cells expressing a gene, UMI is fine. However, if you plan to compute the average expression within a cell type, or any other, I recommend using log1p(CPM). The same applies for using distinct communication scores: if you are using continuous ones it's better using log1p(CPM). Also, it is important that your cell type annotation is done after batch-effect correction if you have multiple samples.

I hope this helps!

Answer 2 · 2023-03-20T15:01:19.000Z

Hi, thank you for the help!