I am comparing expression values in paired samples given a continuous variable. In theory, I should see an increase in expression given an increase in the total score between the paired samples.

This is the code that I have generated to run the analysis. I am using the section "9.4.1 Paired Samples" of the limma user guide as a reference.

```
ID <- factor(mSetSqFlt$Collaborator.ID)
Visit <- factor(mSetSqFlt$TimePoint, levels = c("Baseline","Followup"))
Score <- factor(mSetSqFlt$Total.Score)
design <- model.matrix(~ID + Visit + Visit:Score)
fit <- lmFit(mVals, design)
fit2 <- eBayes(fit)
topTable(fit2, coef = "VisitFollowup")
```

I get outputs using this method and would just like some insights into if I am on the right track.

Any insights would be very much appreciated as I am new to limma.

Thank you for your help, Dr. Smyth. I appreciate your insights and I will adjust my analysis as you recommend.