I have an experiment that has 3 treatment groups (A, B and C) using 3 different cell types (WT, OE, KD).
I am interested to get the result of: within WT, whether the treatment effect is significant? I am not trying to know whether B vs A or C vs B etc are significant, but want to get the result similar to ANOVA.
How to get the result for OE cells and KD cells?
Similarly, I wonder within treatment A, B, and C: whether the 3 cell types are different?
I have been searching for so long but cannot find a good result for my question. I have tried (and probably made the question more complicated):
dds <- DESeqDataSetFromMatrix(countData = cts,
colData = coldata_filtered,
design = ~ Treatment + Cell + Treatment:Cell)
dds <- DESeq(dds)
I found that many forums said it can be tested by the LRT of the reduced model: ~ Treatment + Cell. But how to extract the overall Cell effect within treatment A, B, and C?
