Hello, I have EPIC methylation data. This data is paired: we have two samples for each individual subject (one at timepoint 1, the other at timepoint 2). Some of these patients have a condition, others are healthy. I'm interested in the change in methylation at timepoint 2 versus timepoint 1 comparing diseased vs healthy people. There are 82 paired subjects, 164 total samples. Each of the variables is recognized as a factor.

I am having issues with SVA. I have set up my mod and mod0 matrix to adjust for the effects of patient not attributed to time or condition. However, I am receiving an error and am not exactly sure what it means.

mod <- model.matrix(~0 + ID + Time:Condition,data = pd) #interested in average effect of condition within each timepoint
mod0 <- model.matrix(~0 + ID, data = pd) #adjust for effect of individual patient
SVA <- sva(dat,mod,mod0,vfilter=10000) ##vfilter for reducing time 
Error in solve.default(t(mod) %*% mod) : 
  Lapack routine dgesv: system is exactly singular: U[85,85] = 0

The simple answer is that your mod design matrix is not full rank. You probably need to do something similar to section 3.5 in the edgeR User's Guide in order to make it full rank.