Hello guys! I would really appreciate if someone could help me with DE analysis. This is my challenge:
I have four conditions and I have five biological replicates for each condition. Performing a PCA (DESeq2) we can observe that most of the replicates don't cluster together. My first question is, can I simply analyze them using DESeq2 or edgeR or this would be wrong because of this replicate scenario? Second, are there any ways to filter out the genes in which the replicates are not good and keep only the ones that are consistent among the replicates of the same condition to run the DE analysis?
Thank for the help!