I have 79 samples composed of volunteers who received 5 different treatments. The data resembles the following:
I wanted to answer the question if the difference between the BG and AG of a treatment significantly different from that of another treatment. Is there a way to do a paired difference analysis using deseq?
I've used the following to answer a similar question: For each treatment, is there a significant difference of composition between the BG and AG samples?
dd_tb$group = factor(paste0(dd_tb$Treatment, dd_tb$Status)) design(dd_tb) = ~ group aq_res = results(dd_tb, contrast = c("group", "AqAG", "AqBG")) cr_res = results(dd_tb, contrast = c("group", "CrAG", "CrBG"))
But this question compared the status differences per treatment. Are there any suggestions regarding how I can test if there's a difference among the BG and AG (status) differences between treatments?