I have a general question about normalisation.
A collaborating group has performed RNA-seq on 15 samples - three different groups, 5 samples each. Now they realised that they are only interested in a two group comparison though and they told me to forget about the third group. My question now is the following: should I normalise (I am using TMM) only the samples from the 2 groups I want to compare or still all of them together since they were measured together and belonged to the original experimental design?
I am grateful for advice.