Dear Lluís R, Hi
It is a very interesting topic you have started, and thank you because of that.
I think the design of sampling has a key role here, too.
For example searching for the sex-biased genes, I have compare male and female gonads of different sexes of fish (with biological replications) and in the PCA test there was not something very clear separated, maybe one reason is because the majority of the genes that are expressing in the gonad of two sexes are autosomal genes (and maybe we must not expect such PCA at all in these situations)!
Again, in the regard of DEG analysis and FDR and fold-change, the genes with very sharp FC and expression was related to stress response (maybe the stress the fish has encounter) not the sex differentiation. So the climax of the volcano plot did not contain very interesting news for us!
In other experience, we have used several DEG analysis software (e.g DESeq, DESeq2, voom, edgeR and . . . ) and some of them showed DEG with stronger biological concept than the others. So this fact that which package you are using may have some effects of next steps of analysis.
Finally, if there is no DEG analysis pipeline, which threshold should we consider for trapping the genes that dictate a trait/situation and what would be our "start point" ?
And please have a look at this beautiful paper, specially the part below:
"This analysis revealed that a factor even more important than mouse genotype was the experimenter performing the test, and that nociception can be affected by many additional laboratory factors including season/humidity, cage density, time of day, sex and within-cage order of testing."