Deseq2 question of a single factor with 3 levels
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3.3 years ago
maje • 0

Hi, I am a RNA-seq beginner. Recently, I have a RNA-seq project. There is one factor with 3 levels (A, B, C). Level A is tumor (9 biological replicates); B is tumor + treatment (8 replicates); C is control (6 replicates). I want to compare:

tumor vs tumor+treatment (I know how to do this) tumor vs control (I know how to do this)

Then I want to compare the overlaps of the the above: A+C vs B+C.

samples <- data.frame(row.names=colnames(countMatrix), treatment=as.factor(rep(c("A","B","C"),c(9,8,6))), condition=as.factor(rep(c("AB","AB","C"),c(9,8,6))))

colData<-pData(data)[,c("treatment","condition")]

countData<-counts(data)

dds <- DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~treatment+condition)

dds$treatment <- relevel(dds$treatment, ref="C")

dds<-DESeq(dds)

Many thanks.

RNA-Seq R gene sequencing • 2.8k views
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Instead of trying to translate your experiment into a statistical structure, please post the actual biological setup and comparisons that you'd like to make. We can then translate that into the language of contrasts and statistical models for you.

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The post was edited. Hope it is clearer. Thanks.

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Exactly what do you mean by "overlaps" in your question?

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This post was cross posted at Bioconductor which means volunteers have to answer a question twice.

Deseq2 question of a single factor with 3 levels

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@Michael: You appear to have linked this thread when you meant to link the bioconductor one.

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I apologize. This is my first post on this website. I do not know Bioconductor is the same website. I already deleted another post.

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It's not the same website, but you are making two communities "work" /spend their time on your question, which is a waste of energy for volunteers.

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Does this website have a formal policy on etiquette for crossposting?

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What WouterDeCoster wrote is essentially the policy, though it's never been explicitly written in the FAQ.

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It may be time to consider this.

Although I agree that most people who crosspost without explicitly saying it is a crosspost necessitate unnecessary work for the community, it is also the case the crossposting can help internet communities provided that those queries are linked. Therefore although a posteriori such posters are problematic; a priori I cannot see an issue unless one or both websites have official policies.

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Yes, the issue is mitigated by cross-linking. It's also mitigated by asking serially on one community and then another (provided one allows reasonable time for a reply). What we most have a problem with are people who blast the same question to multiple sites at the same time and never (A) link or (B) provide updates regarding replies from one community in another. That does waste people's time.

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We could write such guidelines in a FAQ document (and we've talk about this in multiple earlier threads) with the main issue that most (new/casual) users aren't going to read those anyway. So we do our biostars police duty and try to educate users about nice etiquette for Q&A forums...

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