I have samples from many different bulk RNA seq studies that exhibit an evident batch effect (samples from different labs cluster together regardless of treatment). I've found a lot of papers (here, here, here. There are many others) that address the batch effect problem for scRNA seq (using many different methods from deep learning to more simple approaches) but I can't find anything that talks about which methods apply to bulk RNA seq. I've also read that some methods that apply to scRNA seq may apply to bulk RNA seq, but with no mention of which methods. I was wondering if anyone can point me to any work on this / any methods used for scRNA seq that can be applied to bulk RNA seq.

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    $\begingroup$ What is your end goal? $\endgroup$ – haci Jun 10 at 19:25

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