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Question: Deseq2 Interaction Term to catch
0
gravatar for guipagui
11 weeks ago by
guipagui0
guipagui0 wrote:

Hi,

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 :

Méthode B

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,

ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by guipagui0
1
gravatar for Michael Love
11 weeks ago by
Michael Love20k
United States
Michael Love20k wrote:

Please look at the diagram in the vignette in the section on interactions.

The most recent DESeq2 question on the support site had the exact same question.

Above you are mixing up main effects and interactions. The interaction is not a main effect, but a difference between the two condition effects.

ADD COMMENTlink written 11 weeks ago by Michael Love20k

Thanks a lot,

The test :

res = results(dds, name="genotypeMU.conditionTrt")

answer to question "Effect of treatment for the 2 genotypes" ? is right ?

https://rpubs.com/ge600/deseq2

I don't see how make it with methode B ... ? it's possible ?

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by guipagui0

No it’s much more difficult to test the interaction with method B.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by Michael Love20k
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