If I only select samples based on their clustering in heatmaps, am I not creating a bias ? For example, I had 35 samples (RNA Seq) nitially, but, in the end, we only selected 12 samples based on their clustering. When I checked for some of the genes in both cases, they were hugely varying in terms of P-adjusted value.
I mean, I know this is a bias but how do I explain this to my boss? Please Helpppp!!!