Hello.
I intend to perform three contrasts including: i) mock.24h vs mock.4h; ii) S2.24h vs S2.4h and iii) the difference between these two comparisons (S2.24h vs S2.4h) - (mock.24h vs mock.4h). The design of my colData is as follows
condition time group
S2 4h S2.4h
S2 4h S2.4h
S2 24h S2.24h
S2 24h S2.24h
mock 4h mock.4h
mock 4h mock.4h
mock 24h mock.24h
mock 24h mock.24h
To address this, I have provided the following design, but I am not sure if these are correct.
design(dds) <- ~ group
dds <- DESeq(dds)
resultsNames(dds)
# e.g. for group mock.24h vs mock.4h
results(dds, contrast = c("group", "mock.24h", "mock.4h"))
# e.g. for group S2.24h vs S2.4h
results(dds, contrast = c("group", "S2.24h", "S2.4h"))
# e.g. for difference group (S2.24h vs S2.4h) - (mock.24h vs mock.4h)
results(dds, contrast = c("group", c("S2.24h", "S2.4h") - ("mock.24h", "mock.4h")))
What would be the most correct way to make this kind of contrasts? I look forward to reading your answers.