Hello, I want to use combat to remove batch effct. The format of rnaseq data is counts from RSEM. The documention of sva package said data should be normalized before using combat. So, how to normalize the data? I want to get counts after removing batch effect for subsequent differential analysis (DEseq/edgR). But DEseq and edgR needs raw counts as input, not TPM/FPKM. What should I do? Best, Zhao
What evidence do you have that a batch effect exists? I would avoid the use of ComBat. You can simply include
batch as a covariate in your design formula and perform differential expression analysis in that way.
So, what I am saying is this: you do not have to use ComBat. If you believe that a batch effect exists, include the
batch covariate in the design formula.