Question: Deseq2 question of a single factor with 3 levels
0
gravatar for maje
4 months ago by
maje0
maje0 wrote:

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.

sequencing rna-seq R gene • 358 views
ADD COMMENTlink modified 3 months ago • written 4 months ago by maje0

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.

ADD REPLYlink modified 4 months ago • written 4 months ago by Devon Ryan79k

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

ADD REPLYlink written 3 months ago by maje0

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

ADD REPLYlink written 3 months ago by Devon Ryan79k

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

ADD REPLYlink modified 3 months ago • written 3 months ago by Michael Love1.6k
1

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

ADD REPLYlink written 3 months ago by genomax47k

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

ADD REPLYlink written 3 months ago by maje0

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.

ADD REPLYlink written 3 months ago by WouterDeCoster28k

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

ADD REPLYlink written 3 months ago by Vincent Laufer890

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

ADD REPLYlink written 3 months ago by Devon Ryan79k

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.

ADD REPLYlink modified 3 months ago • written 3 months ago by Vincent Laufer890
1

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.

ADD REPLYlink written 3 months ago by Devon Ryan79k
1

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...

ADD REPLYlink written 3 months ago by WouterDeCoster28k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 935 users visited in the last hour