I am pretty new to DESeq2. I have read the manual and many question posts, but am still not sure if my design is appropriate or not. Could anyone help me with it?
I have samples from 2 tissues (kidney, liver) with 2 treatment condition (control, Drug) at 2 timepoint (1day, 5days). There are 3 replicates for each situation showing as below.
I'd like to see 1) the effect of the treatment across time in the two tissues and 2)the treatment effect between liver and kidney.
My first design is
dds <- DESeqDataSetFromHTSeqCount(sampleTable=meta, directory=InFolder, design=~treatment+time+tissue+treatment:time)
dds <- DESeq(dds, test="LRT", reduced=~treatment+time+tissue)
 "Intercept" "treatment_treatment_vs_control"
 "time_5days_vs_1day" "tissue_liver_vs_kidney"
To answer question 1), I use res <- results(dds, contrast = list(c("time_5days_vs_1day", "treatment_Drug_vs_control")), test="Wald"). But I think it is for kidney. How do I get the effect for liver when I don't have an interaction term between tissue and other things? Or should I use design=~treatment+time+tissue+treatment:time+treatment:tissue instead? If it is the case, is it correct for me to use "reduced=~treatment+time+tissue+treatment:tissue"?
I tried both and the results are a little different, which one is correct?
To answer question 2), can I just use the "tissue_liver_vs_kidney" results with "reduced=~treatment+time+tissue"? Or do I need to use "tissue_liver_vs_kidney" with "reduced=~treatment+time+treatment:time"?
Please let me know if my design is appropriate for my purpose.
Thanks a lot!