I am looking at treatment as a factor with three levels; baseline, treated, untreated. My dds design included treatment, and genotype. Now i want to focus on the treatment contrast between treated and untreated.

I can export the csv file i saved for the contrast results between treated vs untreated and convert it into data frame but this can not be used for normalization. And hence I can not make a heatmap. Would it be fine to go back and make a datasetmatrix between treated and untreated samples only?

Thanks!