From the vignette of DESeq2, I can either set the factor level by doing this code
dds= relevel(dds$condition, ref=“untreated”)
Or I can use the contrast,
res <- results(dds, contrast=c("condition","treated","untreated"))
“using contrast will additionally set to 0 the estimated LFC in a comparison of two groups, where all of the counts in the two groups are equal to 0”
It’s not clear to me what means“the counts in the two groups are equal to 0”, how can it be 0 counts?
Makes more sense when it says that can be used to test if the difference between two groups is 0
Maybe the contrast function is useful when I have at least three groups to see the different combination between them, let say I have A, B and C , and the set up will be like:
In order to have the combination of the four log2FC, is that correct?