Hello,

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?

Thanks