Hi,

I have a question about biological replicates and technical replicates: In my project, there are four animals for each genotype (hom, het, wt). For each animal, 3 to 4 samples were isolated for RNA extraction. In this case, I do not know for the samples from the same animal, should I consider them as technical replicates and use the DESeq2 collapseReplicates function to collapse data?

e.g. For the Hom group, there are No.2/7/8/12 four animals. For each animal, there are 4 prefrontal cortex samples isolated (e.g. 20/21/22/23 for No.2 rat).

Yes, replicate samples from the same animal should be combined.