A newbie's quandry: It seems to me that in order to decide that a sample is an outlier (and not an unusual biological phenomenon), one always has to use some reasons that have to do with QC.
For example, a sample can be decided to be an outlier based upon low alignment percentage, low reads amount, or anything that signifies a technical problem.
If there is no technical problem, then should not really remove a sample from the analysis no matter how different it is from the others.
If there is no technical problem, and no reason to suspect one, then any decision to remove a sample on biological grounds, would be ultimately impossible to distinguish from fitting the data to support your own hypothesis.
Do you agree?