I have two RNA-seq count datasets as following:
dataset A contains 3 samples and 3 controls
dataset B contains 81 samples with no controls
what is the best workflow to handle the preprocessing in this case:
A- remove batch-effect (for merged dataset) >>>>> quantile Normalization.
B- quantile Normalization (for merged dataset) >>>>> batch-effext removal.
C- quantile Normalization (for each dataset separately) >>>>>>> batch-effect removal.
Thank you in advance.