We have paired samples where cell lines from three individuals were treated with a peptide. Treatment with peptide compared to controls using DESeq2 default Wald's test did not bring any significant DEGs (genes padj > 0.9).
model: ~ individual + treatment
So I tried to test differential expression with LRT
full model: ~ individual + treatment
reduced model: ~ treatment
and got significant DEGs showing consistency with the literature.
Is it correct to use LRT here? I would really appreciate your comments.
Dear Michael,
Thanks for replying and correction.