Using data with batch effects in Sierra about sierra

[rj-patrick]

Hi @hkarakurt,

I wouldn't recommend using Sierra to compare different experiments where there are batch effects, you're likely to get false positives. And definitely not if the technologies are different.

My only recommendation if you want to compare experiments, would be if you had a constant reference cell type in each experiment, that this could be used as an 'anchor' such that your DTU analysis was done within each individual experiment and the gene lists then compared.

Cheers,
Ralpj

[hkarakurt]

Thank you for your answer.
I will definitely try this method.

Have a good day.