Question: Deseq: Multiple Conditions Testing
3
gravatar for k.nirmalraman
6.5 years ago by
k.nirmalraman1.0k
Germany
k.nirmalraman1.0k wrote:

I am finding it a bit hard to comprehend a case where multiple conditions are to be compared and find myself confused with the multifactor part of the DESeq Vignette..

Basically I have four tissues (conditions) and would like to find DE genes for all pairwise comparisons across all conditions. Is the following pairwise comparison approach in DESeq right?

>design
condition    libType
 1            single-end
 1            single-end
 1            single-end
 1            single-end
 1            single-end
 1            single-end
 1            single-end
 1            single-end
 1            single-end
 2            single-end
 2            single-end
 2            single-end
 3            single-end
 3            single-end
 3            single-end
 4            single-end
 4            single-end
 4            single-end
 4            single-end
 4            single-end
 4            single-end


cds <- newCountDataSet( ceiling(RawCountData), conds )
cds <- estimateSizeFactors( cds )
sizeFactors( cds )
cds<-estimateDispersions(cds)

#contrasts for differential expression in DE
 res12<-nbinomTest(cds,1,2)
 res13<-nbinomTest(cds,1,3)
 res23<-nbinomTest(cds,2,3)
 res24<-nbinomTest(cds,2,4)
 res34<-nbinomTest(cds,3,4)

Any better ways of doing it? Also as an extension, I am not sure yet, if the condition 1 and 4 have different time points (which I presume to be, however, I am not interested in time point specificty), will this by any chance change the approach?

Thanks!

ADD COMMENTlink modified 6.5 years ago by Charles Warden7.5k • written 6.5 years ago by k.nirmalraman1.0k
4
gravatar for venkateshr89
6.5 years ago by
venkateshr89710
United States
venkateshr89710 wrote:

Hi,

It looks fine. But I guess if you read in your conditions as vector/matrix that would make life easier. Btw I am wondering if you are doing it that way?

ADD COMMENTlink written 6.5 years ago by venkateshr89710

Thanks!! That reassured... Yes, I am reading it as a phenoData Matrix and using it as vector

ADD REPLYlink written 6.5 years ago by k.nirmalraman1.0k
2

Perfect! I have never done DESeq with pairwise comparison but I have used DEXSeq which is almost same as DESeq. I guess you are doing it right. Good luck.

ADD REPLYlink written 6.5 years ago by venkateshr89710
1
gravatar for Toni
6.5 years ago by
Toni10
Toni10 wrote:

Is there any way to test for differential expression of all four conditions together instead of pairwise?

ADD COMMENTlink written 6.5 years ago by Toni10

It would be quite good to know that! I've been trying to find that out as well 

 
ADD REPLYlink written 5.6 years ago by Diana800
1
gravatar for Charles Warden
6.5 years ago by
Charles Warden7.5k
Duarte, CA
Charles Warden7.5k wrote:

If you have multiple variables, you can use the GLM function in DESeq.

Linear regression can provide the analysis that you are looking for, so I would assume you could use the DESeq implementation to model a single factor with 4 levels. See the overview starting at page 10 for a description of the multi-factor analysis in DESeq:

http://bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf

ADD COMMENTlink written 6.5 years ago by Charles Warden7.5k
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