I have received extraordinary help on this website, and while I have learned a lot about limma, I am still a beginner and am trying to overcome certain limitations. I am trying to determine the effect of a condition within and between the sexes, and one limitation is that I do not feel comfortable implementing my paired study as a factorial design. I do feel comfortable using duplicateCorrelation() and treating my blocking factor as a random effect, and I have 118 patients/236 samples, so I believe my large sample number allows for this without too much loss.
***I am wondering, though, if the duplicateCorrelation() function blocks both between and within samples. If I use duplicateCorrelation() blocking for my patient variable, should I still adjust for my other covariates in my design matrix, or does blocking on that variable implicitly adjust for other factors between patients?***
Any guidance would be much appreciated!
tl;dr does duplicateCorrelation() adjust for differences within and between samples? should I still adjust for other covariates in my design matrix?