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