22 days ago by
In principal yes - you would just have to argue why you would use something else (and you might need to prove the second hypothesis - for most studies the doctors are very carefully with that kind of thing).
In practice this is a lot harder because of batch effects. When a RNAseq experiment is done there is a large effect of the specific day, person age of chemical, protocol used etc - this effect is revered to as a batch effect. This mean that if the samples you want to compare was done in multiple batches you need to correct for this using batch correction (or building more elaborate models).
In your case it means that you cannot take a set of samples from one condition in one study and compare it to samples from another condition in another study because you can never distinguish what is the true effect and what is the batch effect. So in practice no.
If not properly handled this is what happens.