I would like to use DESeq2 for my DE analysis. I have a quite big dataset of about 200 samples, divided into 16 treatments. For each treatment, I have 3 biological replicates and 4 time points.
Because of space issues, we decided to split our samples over 3 different blocks. In each block, we had 1 biol rep for all treatment and all time points.
After data exploration, It is evident we need to perform a batch correction, and for this reason, I would not be able to use raw data as input for DESeq2.
Do you have any suggestions on packages that will still allow me to use it or if there is a way to correct my data within DESeq2?
Thank you very much.