Hello everyone, I have 9 RNAseq samples(human), each with 3 replicates. I have performed the read mapping with STAR and quantification with RSEM. The differential expression(DE) study was performed by EBSeq, DESeq2 and limma. To keep our downstream analysis as stringent as possible, we decided to select the overlapped genes between these 3 algorithms. We have got a good overlap(57.3%) between these 3 methods
What my questions is....... 1) Can we go ahead with the overlapped genes? Is this scientifically right?
2) Or should I just select one from the three and then go ahead with it? if yes, then why?