I need some help with removing batch effects. I have 21 samples 11 samples sequenced in batch A and 10 sample in Batch B. Both batches have both genotypes to compare.
So, In order to perform further downstream differential expression analysis, i need batch adjusted count matrix. How can i get this. i tried combat, limma removeBatcheffects() but it gives negative values for zero counts.
Can i use batch adjusted matrix as a count matrix and perform DEA.
Thanks in advance.