Hi,
I want to do differential expression between two groups(two batches).For clustering analysis of these samples from two groups,I did batch normalization using COMBAT (sva package)on expression values so as to remove batch effects.
But for differential expression,should I do batch normalization as well before proceeding, as DEseq expects raw counts ? Or is there any way DEseq bioconductor takes into account for different batches and does normalization,before doing differential expression?
Any suggestions,please?
Thanks,
Ron