I have been trying different methods to identify immune sub-populations.
For cell identification in general, the most commonly used method in papers seems to be SingleR, others cluster and define different clusters based on the most HVGs.
Since there is no gold-standard to this date, I have tried SingleR with different references (fine labels), ProjectTIL, scPred, and identifying markers for different clusters - but across these methods none agrees! For major labels this is less of a problem.
So for example, how can I justify, or any paper as a matter of fact, that a cell is a T Cell CD4 Effector Memory if across all these methods none of the labels agree? Do people just decide to base cluster or cell annotation using the method that fits their bias best? Would be great to hear some opinions to know how to move forward with cell subtype identification in my data. Thank you!