I have two RNA-seq experiments that I have done separately with different tissues (tissue 1-4) and different conditions (treatment 1 and treatment 2).
Initially, I want to compare the tissue types within each experiment (eg, tissue 1 vs tissue 2, etc, all under treatment 1 or treatment 2).
But now I was thinking is it possible to compare the same tissue type between experiments (eg. treatment 1 vs treatment 2 of tissue 1 etc.).
I had a look at other people's posts, some were talking about combing and how to remove the batch effect, etc. But I want to know how to combine two RNA-seq data or DESeq objects (i have the dds from both expts). Is there a function in DESeq2 that can do that? Or shall i combine the normalized counts from both expts, then use the DataFromMatrix function?