I am doing differential gene expression of 5 different subjects, 2 treatments, 2 time points. I want to combine the response of the treatment at both time points, but controlling the subject effect. I am not interested in the effects across the subjects or to each time point.
Not sure how to do it,
Now I have:
dds <- DESeqDataSetFromMatrix(
countData = countdata,
colData = coldata,
design = ~Time + Treatment)
dds$Treatment <- factor(dds$Treatment, levels=c("35", "25"))
dds$Treatment <- relevel (dds$Treatment, "35")
dds$Time <- factor(dds$Time)
dds <- DESeq(dds)
But I think this is not taking into account my subject ID? I looked at the contrast option but I understand this is for looking at differences within the factors.