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wguo-research / scCancer

A package for automated processing of single cell RNA-seq data in cancer
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Use 'data' for estimating ligand-receptor pairs #9

Open Puriney opened 4 years ago

Puriney commented 4 years ago

Hi,

https://github.com/wguo-research/scCancer/blob/3f9eb9e878531d588594a132f00d60d6d38506c8/R/scAnnotation.R#L1325-L1326

Here it uses the 'counts' slot , i.e., UMI, to estimate the strength of ligand-recept pairs. I was wondering if it is making more sense to use 'data' slot , i.e., normalized data.

wguo-research commented 4 years ago

I consider it in this way. I think the interaction strength between a ligand-receptor pair is only related to two genes (proteins), but normalization will make this strength influenced by other genes due to the use of relative expression.