I have two groups with 3 replicates each for differential gene expression analysis.
Control - Sample1 - Sample2 -Sample3
Experiment -Sample1 -Sample2 -Sample3
However, Sample3 in Control has high duplication rate almost double reads than other samples. For differential gene expression in Deseq2, can I exclude the Sample3 in control and compare Controls (Sample1, Sample2) vs Experiment (Sample1, Sample2, Sample3). Will Deseq2 library size normalization take care of unequal sample sizes?
When I am doing DGE with n of 3 I get really low number of significant DGEs (Differentially expressed genes). But when I do n of 2 I get much higher DEGs. Or should I report differential expression results for n of 2 only. Is n of 2 statistically significant?