Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • edgeR issue:RNA seq

    I am facing an error at the step Trended Dispersion, although no error during Common dispersion estimation.

    rownames(design) <- colnames (d)
    > z<- estimateGLMCommonDisp(d , design)
    v<- estimateGLMTrendedDisp(d , design)
    Error in t(y) + prior.count.scaled : non-conformable arrays

    Please suggest what could be the reason, and what would be the way out.

  • #2
    do I have to edit aveLogCPM.default, if yes, then How?

    Comment


    • #3
      I think

      v<- estimateGLMTrendedDisp(d , design)

      should be

      v<- estimateGLMTrendedDisp(z , design)

      ie you have to run CommonDisp on 'd', and then run TrendedDisp on the output of that.

      Comment


      • #4
        Ok.. yah.. Thanks. I was making some silly input mistake in some earlier step too. That step, including your suggession make it work properly. But strangely, all 20 top tags are showing Downregulation in disease. That has made me a bit sceptical. I am doing double check now.

        Thanks

        Comment


        • #5
          Good that it works; to check your top 20 tags I suggest you look at FPKM/RPKM or raw counts to make sure the 'direction' of regulation is correct. EdgeR gives "-logFC" for the first condition you provide IIRC. This can be confusing, and I still double check all results against FPKMs.

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Best Practices for Single-Cell Sequencing Analysis
            by seqadmin



            While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
            06-06-2024, 07:15 AM
          • seqadmin
            Latest Developments in Precision Medicine
            by seqadmin



            Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

            Somatic Genomics
            “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
            05-24-2024, 01:16 PM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 06-17-2024, 06:54 AM
          0 responses
          11 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 06-14-2024, 07:24 AM
          0 responses
          23 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 06-13-2024, 08:58 AM
          0 responses
          17 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 06-12-2024, 02:20 PM
          0 responses
          20 views
          0 likes
          Last Post seqadmin  
          Working...
          X