I read the documentation, vignette, tuto ... but i'm face an issue.
Let's try :
dds <- makeExampleDESeqDataSet(n=10000,m=12)
dds$condition <- factor( c( rep("Ctrl",6), rep("Trt",6) ) )
dds$genotype <- factor(rep(rep(c("WT","MU"),each=3),2))
dds$genotype = relevel( dds$genotype, "WT")
If i want to modelise the effect of treatment for genotypes:
Méthode A :
design(dds) <- ~ genotype + condition + genotype:condition
res = results(dds, name="genotypeMU.conditionTrt")
that's ok but :
dds$group <- factor(paste0(dds$genotype, dds$condition))
design(dds) <- ~ group
res = results(dds, name="group_WTTrt_vs_MUCtrl") doesn't give the same result
What's i'm wrong ?
Thanks a lot,
The test :
answer to question "Effect of treatment for the 2 genotypes" ? is right ?
I don't see how make it with methode B ... ? it's possible ?
No it’s much more difficult to test the interaction with method B.