Hello, I have a time course RNAseq experiment (2 trt x 5 time points), and I want to find differences in gene expression levels over time for both treatments. I specified the experiment in terms of a factorial model:

```
design <- model.matrix(~trts * time, data=trtstr)
```

And, I got the following coefficients

```
"(Intercept)" "trtsTRTB" "time14d" "time1d" "time22d" "time7d" "trtsTRTB:time14d" "trtsTRTB:time1d" "trtsTRTB:time22d" "trtsTRTB:time7d"
```

I'm interested in the following contrasts:

```
my.contrasts <- makeContrasts(TRTAvsTRTB.0d = TRTA.0d-TRTB.0d,
TRTAvsTRTB.1d = (TRTA.1d-TRTA.0d)-(TRTB.1d-TRTB.0d),
TRTAvsTRTB.7d = (TRTA.7d-TRTA.0d)-(TRTB.7d-TRTB.0d),
TRTAvsTRTB.14d = (TRTA.14d-TRTA.0d)-(TRTB.14d-TRTB.0d),
TRTAvsTRTB.22d = (TRTA.22d-TRTA.0d)-(TRTB.22d-TRTB.0d), levels=designB)
```

Will `qlf <- glmQLFTest(fit, coef=7:10)`

equivalent to these contrasts?

Also, will the model.matix account for sampling from the same individual at different times?

Thanks,

Yes, it is easier to understand. I was making sure the contrasts were equivalent to coefficients used in the previous analysis. Thank you for the clarification! Do you have any suggestion on how to account for repeated measurements from the same individual in an RNAseq experiment?