text: user15643: I have 3 groups for the RNA-seq analysis (Control, treatment A and treatment B). There are 2 replicates for control and treatment A and 3 replicates for treatment B (lost 2 replicates due to a mistake in sample handling). May I ask how will the inconsistent replicate numbers impact the results (e.g. DEGs)?
  
  user16676: It will not do any harm other than a reduction in statistical power compared to more samples per group. Common analysis tools such as DESeq2, edgeR and limma will work on unequal sample size just fine.
  
original_text: 15643: <p>I have 3 groups for the RNA-seq analysis (Control, treatment A and treatment B). There are 2 replicates for control and treatment A and 3 replicates for treatment B (lost 2 replicates due to a mistake in sample handling). May I ask how will the inconsistent replicate numbers impact the results (e.g. DEGs)?</p>
   16676: <p>It will not do any harm other than a reduction in statistical power compared to more samples per group. Common analysis tools such as DESeq2, edgeR and limma will work on unequal sample size just fine.</p>
  