Deseq2 Interaction Term to catch
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Entering edit mode
guipagui • 0
@guipagui-17517
Last seen 3.1 years ago

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,

deseq2 interaction term • 338 views
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Entering edit mode
@mikelove
Last seen 2 hours ago
United States

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.

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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 ?

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Entering edit mode

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

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