I am performing differential expression analysis using RNA-seq data. I am using limma package.
I am wondering to know how I can bias my differential expression analysis if previous to differential expression test I use Combat to correct for batches effects although there is no clear evidence of batch effect when I plot data into a PCA/heatmap... However, I know that this batch (library prep) can influence my expression level.
Would it be a better approach to include the batch in the model?
Thanks for your help!