I'm using DESEQ2 to calculate differential expression of genes. My data can be best seen through my metadata file which looks like this:
projectname Line Treatment 1 LineX DoseA 2 LineX DoseA 3 LineX DoseB 4 LineX DoseB 5 LineX Untreated 6 LineX Untreated 7 LineY DoseA 8 LineY DoseA 9 LineY DoseB 10 LineY DoseB 11 LineY Untreated 12 LineY Untreated
I want to get differential expression for DoseA vs Untreated, and DoseB vs Untreated, for each Line separately, so in total I would have 4 results tables.
I did this with subsetting the original table everytime before I did the DESEQ2 analysis, but I want to get better results with normalizing all the samples together, and subsetting only when calculating the differential expression. How is this possible?