Hi all, 

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

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. 

DESeq2_1.4.5 

Thanks,

Catalina

hi Catalina, 

Just a note, you're 2 version behind the release (1.8) and we recommend keeping up to date if possible (it is not always possible in the middle of a project which relies on other package versions).

I would need to see the column data to see if it is possible to control for subject across treatment:

as.data.frame(colData(dds))

If subject effects are not confounded with treatment you could use: ~ subject + time + treatment

Another small note: giving the level order to factor() means that you don't have to use relevel() because you've already specified the reference level.