Sample level integration of two RNASeq datasets

Question

[Kristoffer Vitting-Seerup]

I'm interested in doing a sample level analysis between two different datasets (which samples is dataset B is more/less similar to sample A and vice versa). Naturally the two datasets will cluster completely separate due to being different biological samples and the batch effect - so the question is how do I get the data "on the same page" so I can do a Sample level comparison (aka not gene level). Any ideas, links to previous articles and especially existing tools are wanted!

Cheers Kristoffer