I am looking for statistical expertise to figure out if I have set up my model matrix correctly. I am going to give an example info table that represents my experimental design. I have read the limma and edgeR documentation through and through and cannot find a clear example of this.
DESIGN: 3 individuals with recordings of a treatment at baseline and 3 future time points. baseline is preinfection. timepoints relate to stage in disease progression.I am interested in the differential expression at each timepoint with timepoint 1 being baseline.
PSEUDOCODE (did not run this in R it is a fake example):
file individual timepoint status file <- 1:12 individual <- c(rep(1,4),rep(2,4),rep(3,4)) timepoint <- rep(0:4,3) status <- rep(c("uninfected",4),rep("infected",8)) df <- cbind(file,individual,timepoint,status) model.matrix(~individual+timepoint) model.matrix(timepoint~(1|individual))
The main effect I want to see is the effect between timepoints not individuals- so I understand I can treat the individuals as a random effect in a mixed model. I just am not sure not to correctly integrate multiple independent variables, paired samples, and longitudinal data with baseline measures.
Any help and or explanations would be greatly appreciated!