Entering edit mode
Hello everyone,
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"))
Vignette says:
“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:
results(dds, contrast=c("condition”,”A”,”C”,”B”))
In order to have the combination of the four log2FC, is that correct?
Thank you
Hi Michael, this could happens if there are technical errors during the sample preparation is it that? I mean there are not live organisms with no RNA/DNA ,
is it the code correct the way I did with three groups? condition wil be the column of the txt file where the A,C and B condition are
Is it correct to say that if I set the contrast code I don't have to add a reference when more groups are there because all the combinations will be analyzed ?
thanks