Inquiry on Alternative to 'Stat' in LFC Shrinkage

[yummy11111]

Hello,

Thank you for providing such amazing tools!

I have a question regarding transcription factor (TF) activity analysis in bulk RNA-seq. In my analysis, I used lfcShrink() instead of results() for differential expression analysis to reduce noise in my in vitro data. However, I noticed that when using 'apeglm' for effect size estimation, the 'stat' value is not available.

Given this, which value would you recommend using as a substitute for 'stat' in this context?

I have attached the DESeq2 output, hope it helps clarify my question.

Looking forward to your insights!

Best regards,
Yaqin

DESeq2 output.xlsx