DESeq2 design formula for time - condition - donor

Question

[asilvestris]

Hi, I need advice on how to set up the formula for the experimental design in DESeq2 in a complex analysis in which I have three DONORS and for each I have three TIMES and for each time I have an untreated control and a treated:

The goal of the study is to find genes whose expression varies according to condition and time and independently of the donor. Please I would really appreciate your help. THANK YOU!

Ale

Answer 1

[jared.andrews07]

I believe your design would be:

dds <- DESeqDataSet(dds, design = ~donor + condition + time + condition:time)
dds <- DESeq(dds, test = "LRT", reduced = ~Culture + H3_Status + DaysDiff)

Alternatively, you could collapse condition & time into a single column do pair-wise comparisons at each timepoint.

dds$timecondition <- paste0(dds$time, dds$condition)
dds <- DESeqDataSet(dds, design = ~donor + timecondition)
dds <- DESeq(dds)