I am working with two data sets, e.g., Study "A Ht-seq counts" and Study "B Ht Seq counts". I want to combine these two studies. Since they are two different datasets, I need to correct them for batch effects. Now, my question is should I perform the batch correction on Ht-seq raw counts or normalized counts? And what's the difference between doing the batch correction on Ht-Seq raw counts and the normalized counts?
I just started working with the Ht-Seq RNA-Seq data, so I'm relatively new to this area. I will appreciate any help/advice.