I have a critical question regarding batch effect correction. I have 290 samples on 4 treatments and 41 batches. Batches here are the numbers given for each sequencing run. When I run PCA or MDS plot, I do not see any clustering based on the batch. I do not see any batch clustering even when I run PCA with a smaller number of samples.
I am aware of the technical variability in the RNA-seq. Though my question is this: Do I still need to do batch correction for my DE analysis regardless of PCA ? (due to having a great number of batches in my dataset?
Appreciate your input,