how to specify samples for comparison in dexseq

[camelbbs]

Hi all,

I want to ask how to specify conditions for DEU detection in DEXSeq.

I see in DESeq, after I do estimateDispersion, I can use

res<-nbinomTest(cds,"sample1","sample2")

to specify which conditions I want to compare.

But in DEXseq, I don't see that.

So in DEXseq, do I need to import just the samples I want to compare every time?

Thanks!

[areyes]

Hi @camelbbs,

You could modify the formulas (in estimateDispersions and testForDEU) to specify the contrasts that you want, but its a bit tricky. Subsetting the ExonCountSet object leaving the samples that you want is the easiest.

Alejandro

[camelbbs]

Hi @camelbbs,

You could modify the formulas (in estimateDispersions and testForDEU) to specify the contrasts that you want, but its a bit tricky. Subsetting the ExonCountSet object leaving the samples that you want is the easiest.

Alejandro

I see, Thanks!

[camelbbs]

Hi @camelbbs,

You could modify the formulas (in estimateDispersions and testForDEU) to specify the contrasts that you want, but its a bit tricky. Subsetting the ExonCountSet object leaving the samples that you want is the easiest.

Alejandro

Hi Alejandro,

I suddenly think that in DESeq, do I also need to import two conditions each time to do the estimatesizefactor and estimatedispersions?
can I import all conditions (>=3) together, and then do sizefactor and dispersion together, and then use res<-nbinomTest(cds,"cond1","cond2") to select which two conditions I want to compare?

In DESeq document, I see in the chapter "working partially without replicates", it indicates to do estimatesizefactor to new cds, but in the chapter " working without any replicates", I see there don't need to do that. So What is the affection if I do estimatesizefactor with all or partial conditions, since I see the sizeFactor is different.

thanks a lot!

Ch