processing multiple datasets

[marce-sarrias]

Hello,

I've got a bit of a silly question:

I've got this pretty massive dataset with all sorts of samples, sequenced at different times and on different platforms. So, here's the thing: should I run DegNorm on the whole dataset, all samples together, or should I do it separately for each batch of samples? Does it really make a difference? What's the smartest way to go about it?

I'd be super grateful for your thoughts on this!

Thank you,

Marcela