I want to correct for batch effects. I have two data sets, two similar diseases, measured at completely different time points. When I do PCA, I clearly see two groups; however, this shouldn't be the case since those two diseases are rather similar and therefore, that's a clear indication of batch effects.
The thing is that I'm just getting started with batch effect corrections and therefore, I'm not really familiar with how I should properly do the analysis step by step. Consequently, I would appreciate if someone could shed some light on how I should proceed.
By the way, I have already read the SVA paper by Leek et al. but I didn't really get into the topic or how I should proceed.
Thank you in advance.