Differential gene expression

[rosaluna95]

Hi,

I am currently analyzing my single-cell data using Seurat. I am just confused when I analyze differential gene expression using FindMarker function.

I am getting over 4,000 DEG which is a high number than expected. Does this seem right? I have 18,077 cells and 15,676 features which come to 15,676 features and 2,060 cells when subletting for the findmarker function.

Thank you,

[Lea2609]

4000 DEG with p_val or p_val_adjust ?

[Jiayi-Zheng]

Check the p_val_adjusted and the log2fc, if log2fc is too small or p_val_adjusted too large then it's probably not meaningful. Discard it. I don't usually get that many DEGs with all the filtering i added.