Differentially expressed genes

[zxs132]

Hello, I want to ask about the simulation process as I am trying to mimic the simulation described in the manuscript.

I think the differential expression part is most confusing to me.

Even though I simulated the data as you described in the simulation setup part, I am getting way lower number of DEGs compared to your results in the paper.

I think the difference came in when the DE factor, similar to the fold change, is generated.

There was no mention about the DE factor in the paper, so I left the parameters as default.

Can you please share your code for simulation or at least the parameters you set for the Splatter?

Thank you very much.

Best regards,