Question: questions about DESeq2
0
gravatar for tony.fox2016
4.4 years ago by
tony.fox20160 wrote:

Hi,

I have a couple of questions about DESeq2:

  1. in the DESeq2 workflow, to test the dex treatment effect, the following command was used:

    dds <- DESeqDataSet(se, design = ~ cell + dex)
    

    And I guess the only factor here is "dex" and it might be more straightforward to use:

    dds <- DESeqDataSet(se, design = ~ dex)
    
  2. If I am performing an ANOVA-like comparison of 3 groups A, B and C:

    design(dds) = ~ group
    dds = DESeq(dds, test = "LRT", reduced = ~ 1)
    results(dds)
    

To extract the DE genes between B-vs-A and C-vs-B. We should use the following commands and no post-hoc tests are needed. Is it correct?

res.B.vs.A <-results(dds, contrast=c("group","A","B"))
res.C.vs.B <-results(dds, contrast=c("group","B","C"))

Many thanks for Michael Love and colleagues for contributing such an excellent software and their answers in the forum!

rna-seq • 1.7k views
ADD COMMENTlink modified 21 months ago by RamRS27k • written 4.4 years ago by tony.fox20160

Thank you very much for the answer. It is very helpful. I will post it in bioconductor forum and hope Michael could see it.

ADD REPLYlink written 4.4 years ago by tony.fox20160
0
gravatar for mbio.kyle
4.4 years ago by
mbio.kyle360
United States
mbio.kyle360 wrote:

I'm by no means a DESeq2 expert, but I have been using in my last few projects. In regards to your first question I suppose it would depend on your experimental setup / matrix. If you truly have just one 'treatment' then I believe your design is correct. One way to verify this is to use:

resultsNames(dds)

Which will show you which contrasts have been formed.

As for part two, the results() function will return every single gene, so you will likely want to wrap the call with a call to subset, something like:

subset(results(dds, contrast=c("group", "A", "C"), padj < 0.05)

One final note, I have had much more luck posting questions like these (specific to bioconductor packages) to the bioconductor forum.

ADD COMMENTlink modified 21 months ago by RamRS27k • written 4.4 years ago by mbio.kyle360
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