Hi all,

I have already done the batch correction with design matrix for FC analysis. I want to compare the absolute levels of a gene in the study groups. How can I incorporate batch correction in this comparison? Do I really need to consider batch effect here? My question may sound naive, but I want to know what is done usually in this case. Many thanks

It's not clear what your question is. You say you have adjusted for batch in your design matrix, then ask how to do so, and if it's necessary. Why ask how to do what you say you have already done? Have you done any exploratory data analysis? What does your PCA plot look like?