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)
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?