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  • 4 conditions in DESeq2

    I have four conditions A, B, C, and D that each have three HTSeq count files.

    I want to use DESeq2 to compare A to B, A to C, A to D, B to C, B to D etc.

    With DESeq, I would bring all the 12 files into a countDataSet and then I could specify which of the conditions to compare.

    With DESeq2, I can bring all the 12 files into a DESeqDataSet, but I can not figure out how to do specify the particular comparisons.

  • #2
    It's easy. Use the contrast variable of the results function. Comparing all pairs of contrasts is not a good idea, though. Why don't you have a better biological hypothesis ?

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    • #3
      We have wild type condition A and wild type condition B as well as treated condition A and treated condition B. So, we would like to see changes in gene expression between condition A and condition B, as well as changes in gene expression between wild type and treated.

      Will contrast provide us with this ? To me it seems like the analysis is done by the DESeq function and the results function just organizes the output of the DESeq function.

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      • #4
        Yes, a contrast allows you to perform pretty much any comparison you want. Note that the comparisons to A don't require contrasts, since those are just fit coefficients.

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        • #5
          hi Matt,

          For lots more information about what you want to do, check out the man page for ?results and section 3.2 Contrasts in: vignette("DESeq2")

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          • #6
            Thank you very much for your answers Dario, Devon and Michael !

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            • #7
              > "Note that the comparisons to A don't require contrasts, since those are just fit coefficients."

              Safest always to use contrast=c("condition","B","A"), because when we have expanded model matrices for symmetric shrinkage, then the coefficients are not B_vs_A, but simply A, B, etc. This will be clear from resultsNames(dds)
              Last edited by Michael Love; 01-22-2015, 12:24 PM.

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              • #8
                OK. Thank you for clarifying that.
                (And also for making DESeq2 !)

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