Hello all,

I have two group of samples (control vs drug treated) and within each group, I have three cell lines in biological triplicates. I am interested in the comparison of control vs drug treated. There are two ways to do this differential expression analysis.

1. Assume we have 9 samples in each group (three cell line in biological triplicates) and consider them as the replicate of each other. Then we can simply compare 9 vs 9 samples. However in this way we don't consider biological heterogeneity between cell lines.

2.we have three cell line and three replicates for each and we want to do group comparison like the following

((control - cell line1) and (control - cell line 2) and (control - cell line 3) Vs. (treated - cell line 1) and (treated - cell line 2) and (treated - cell line 3))

So then instead of 9 vs 9 comparison, we do (3+3+3 vs 3+3+3) which consider each cell line as a group and then we compare three groups vs three groups. 

I want to run the second type of analysis but have no idea how to this. Could you please introduce a tutorial for that? Any help would be highly appreciated.

Thanks! 

There is a huge (HUGE!) vignette that covers pretty much everything you need to know about DESeq2, including how to fit a model with blocking factors. If you plan to use the package, you should read the vignette first.