Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • DESeq, elevated SD in lower count range even after VST

    Hi,

    I am using DESeq for differential expression analysis. When I transformed the data for variance stabilization using varianceStabilizingTransformation from DESeq, I still see an elevated standard deviation in the lower count range. Does anyone have come across similar issue? I am using appox. 50 vs 50 replicates. Does large number of replicates creates such elevation?..



    Thanks

  • #2
    Can you share the code/script you used as it might make the issue a bit clearer?

    Comment


    • #3
      Hi,

      I used the code according to the vigenette:

      countTable = read.table("count_data.txt", header=TRUE, row.names=1)
      condition = factor(c(rep("A", 44), rep("B", 21), rep("C", 55)))
      cds = newCountDataSet( countTable, condition )
      cds = estimateSizeFactors( cds )
      cdsBlind = estimateDispersions( cds, method="blind" )
      vsd = varianceStabilizingTransformation( cdsBlind )

      I am also attaching the meanSdPlot. First plot is from log transformed data and the second is from VST.

      thanks,
      Attached Files

      Comment


      • #4
        Could you explain what the numbers and letters refer to in the following line?

        condition = factor(c(rep("A", 44), rep("B", 21), rep("C", 55)))

        I

        Comment


        • #5
          Hi,

          A, B and C are the conditions and the numbers represent the replicates.

          Comment


          • #6
            Wow, thats a lot of replicates, so your initial table has 120 columns? And in the first row 44 of them just have A, 23 have B and 55 are C?
            I've heard of an experiment with so many rep's before so i'm trying to imagine the table structure.

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Recent Advances in Sequencing Technologies
              by seqadmin







              Innovations in next-generation sequencing technologies and techniques are driving more precise and comprehensive exploration of complex biological systems. Current advancements include improved accessibility for long-read sequencing and significant progress in single-cell and 3D genomics. This article explores some of the most impactful developments in the field over the past year.

              Long-Read Sequencing
              Long-read sequencing has...
              12-02-2024, 01:49 PM
            • seqadmin
              Genetic Variation in Immunogenetics and Antibody Diversity
              by seqadmin



              The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
              11-06-2024, 07:24 PM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 12-02-2024, 09:29 AM
            0 responses
            141 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 12-02-2024, 09:06 AM
            0 responses
            50 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 12-02-2024, 08:03 AM
            0 responses
            39 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 11-22-2024, 07:36 AM
            0 responses
            70 views
            0 likes
            Last Post seqadmin  
            Working...
            X