I was just wondering how to correctly deal with the following model design. I want to compare two different cell populations, each taken from the same mouse; 5 replicates each. RNA was extracted in two separate days.
so I have: 2 conditions (population 1 and 2), 5 pairs and 2 batches (day 1 and 2)
should I simply do the following: ~pairs+batches+condition
Am I right?
Thanks a lot for these information. No, the extraction was 'balanced', meaning that I extracted the first three replicates (A and B, then) first and then the remaining ones on the following day. It has been asked to do a paired analysis given the fact cells from each replicates are coming from the same mouse. But what does it mean? How can one do that on DESeq2? I think one should just follow the normal design as usual and that's it, right?
Can you post such a table as above including all the factors that are relevant such as which animal etc.?
That is basically the same as you posted above. Data retrieved from mice.