I have a data set with 3 groups of samples, PD, SD, and CR/PR based on the Response variable. I am interested in finding DEG genes between PD and CR/PR with PD as the reference level.
My design is: design(dds)=~Response
Normally, in order to get the DEG result, I would call results(dds,contrast=c("Response","PRCR","PD")) to retrieve the result. However, I am wondering about the result from calling results(dds,name="ResponsePRCR") which is supposed to give us the individual effect and yet has the all the result columns, baseMean, log2FoldChange, ...
What exactly is this "individual effect"? How do I interpret the result from using name option? What's the difference between using contrast and using name? Thanks a lot.