Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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 ?

    Comment


    • #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.

      Comment


      • #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.

        Comment


        • #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")

          Comment


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

            Comment


            • #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.

              Comment


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

                Comment

                Latest Articles

                Collapse

                • seqadmin
                  Techniques and Challenges in Conservation Genomics
                  by seqadmin



                  The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                  Avian Conservation
                  Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                  03-08-2024, 10:41 AM
                • seqadmin
                  The Impact of AI in Genomic Medicine
                  by seqadmin



                  Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
                  02-26-2024, 02:07 PM

                ad_right_rmr

                Collapse

                News

                Collapse

                Topics Statistics Last Post
                Started by seqadmin, 03-14-2024, 06:13 AM
                0 responses
                33 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-08-2024, 08:03 AM
                0 responses
                72 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-07-2024, 08:13 AM
                0 responses
                80 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-06-2024, 09:51 AM
                0 responses
                68 views
                0 likes
                Last Post seqadmin  
                Working...
                X