Hi all

New to bioconductor and RNA-seq analysis here.

I have 8 groups and 3 samples per group. Each group has been exposed to control and treatment (2 exposures per group for a total of 16 different group-exposure combinations).

Of these 16 combinations, I have 1 combination that I want to make the "control" and get the DE genes for the other 15 combinations relative to this combination. If possible, I want to make a heatmap with this information.

I also have another issue with batch effects. I obtained the 24 samples (3 per group x 8 groups) in 2 batches. Each group has at least 1 sample in each batch. However for the purposes of my project I want to create visualizations of the DE genes after "correcting" for the batch effects.

Is all this feasible? If there is a guide to how to do this, using edgeR/limma/limma-voom/DESeq, could you point me to it?

Thanks