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Question: Interaction with DESeq2 via DiffBind
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gravatar for rbronste
11 weeks ago by
rbronste50
rbronste50 wrote:

Hi wondering how I can use the following DESeq2 logic within the framework of DiffBind for calling differential peaks and looking at multiple interactions:

to look at interaction--
dds<-DESeqDataSetFromMatrix(countData = countData,
                           colData = colData,
                           design = ~ sex + treatment + sex:treatment)
dds$sex<-relevel(dds$sex, ref="female")
dds$age<-relevel(dds$treatment, ref="CO")

dds <- DESeq(dds)
resultsNames(dds)
results(dds, name="sexmale.treatment")
ADD COMMENTlink modified 10 weeks ago by Rory Stark2.2k • written 11 weeks ago by rbronste50
2
gravatar for Rory Stark
10 weeks ago by
Rory Stark2.2k
CRUK, Cambridge, UK
Rory Stark2.2k wrote:

Currently DiffBind only handles fairly simple designs. I'm looking to upgrade this in future, but the original idea was that if you wanted to do more complex modelling, you should use the underlying DE package (DESeq2) directly.

Cheers-

Rory

ADD COMMENTlink written 10 weeks ago by Rory Stark2.2k

Thanks Rory! Would it be fair to use the dba.count output matrix and feed that into DESeq2 via DEseqDataSetFromMatrix?

So as to get around having to manually create a read depth adjusted matrix for all of your peaks?

Thanks again.

ADD REPLYlink written 10 weeks ago by rbronste50
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