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Question: Deseq2: How to compine reseult of different pairwise comparisons
0
gravatar for tarekzakaria.badr
4 weeks ago by
tarekzakaria.badr0 wrote:

Hi,

I've a small question concerning the differential expression analysis in DESeq2. So I've a 16 samples divided into 4 groups (control, ko1, ko2 and ko3 ). so one condition with 4 levels

as i understood form the vignette and previous questions regarding this matter here that performing wald statistics and separata pairwise comparisons would be the best options.

i am using a code like this one:

dds1 <- DESeqDataSetFromHTSeqCount(sampleTable=samples,directory="./",design= ~ condition) dds1 <- DESeq(dds1) res <- results(dds1)

Then pairwise comparison res.ko1 <- results(dds1, contrast=c("condition","ko1","ctrl")) res.ko2 <- results(dds1, contrast=c("condition","ko2","ctrl")) res.ko3 <- results(dds1, contrast=c("condition","ko3","ctrl"))

Now my question is, is it possible in DESeq to get a compined file of the significant DEG in the three cell types containing mainly how is the fold change is. somthing like a list with significant genes and the fold change in each level/ko.

Many thanks in advance

deseq2 • 94 views
ADD COMMENTlink modified 4 weeks ago by Michael Love22k • written 4 weeks ago by tarekzakaria.badr0
Answer: Deseq2: How to compine reseult of different pairwise comparisons
1
gravatar for Michael Love
4 weeks ago by
Michael Love22k
United States
Michael Love22k wrote:

DESeq2 doesn’t have any functionality to combine results from multiple contrasts into a large table.

ADD COMMENTlink written 4 weeks ago by Michael Love22k

Thanks a lot for your feedback and answer. What about normalizing against the control. I couldn't find a clear approach on how to do that. As example i would like to normalize each genotype against the common control then compare them against each other. Is it possible to do that? Many thanks in advance.

ADD REPLYlink written 3 days ago by tarekzakaria.badr0
1

This is asked often, comparing against a control is equivalent to comparing directly unless you have matched control samples. This follows from simple algebra:

(C - A) - (B - A) = (C - B)

ADD REPLYlink written 3 days ago by Michael Love22k

Thanks a lot for your feedback. But what would be the case if i have a matched control specific to each experiment? I tried doing some kinda of a mixed condition as ( ~ condition + genotpye) but it didn't work out with me. Do you have some suggestion on how to tackle this if one needs to normalize against a specific control (as having a specific genotype for each control). So basically doing ((D-C) - (B-A)) ? Thanks in advance.

ADD REPLYlink modified 2 days ago • written 2 days ago by tarekzakaria.badr0

We have an example of paired data in the vignette FAQ, and of matches samples across groups

ADD REPLYlink written 2 days ago by Michael Love22k

We have an example of paired data in the vignette FAQ, and of matched samples across groups in the section on interactions

ADD REPLYlink modified 2 days ago • written 2 days ago by Michael Love22k
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