DEG analysis and cell number(proportion or frequency) comparison in scRNA-seq

Question

[joonhong kwon]

Hi all,

I have a question about the relationship between DEG and cell number (or proportion or frequency) comparison in scRNA-seq. DEG analysis and comparison of cell number were performed to compare control and disease group. When pseudo-bulk DEG analysis was performed using DESeq2, gene A was up-regulated in Cluster X. But cell number of Cluster X was decreased in disease group.

In this case, can it be said that gene A was actually up-regulated in the disease group? Or what if we want to show that gene A expression is increased?

Thank you.

Best,

Joonhong