Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • microRNA normalization

    Hi,

    Does anyone know the reasonable normalization methods for microRNA data analysis?
    I already trimmed adaptor, mapped these reads to the reference, and counted the number of reads that mapped on the known microRNA seq.

    What I have is a list of known mature microRNAs' ID and sequence, and the number of reads mapped to this miRNAs.
    I have 5 samples and want to compare differential expression among them.

    How do you normalize the number of mapped reads in order to compare the results from different samples?
    Any RPKM-like methods?

    Thanks,

  • #2
    Use Deseq just with the raw counts and make diff.expr
    ------------
    SMART - bioinfo.uni-plovdiv.bg

    Comment


    • #3
      Thanks vebaev,
      Do you use Deseq for miRNA expression analysis?
      One of my concern is the number of miRNA I have in my list is small, 300 ~ 800, depending on a category.
      Can I assume that most of miRNA does not change expression levels as we do in mRNA expression analysis?
      I think Deseq is good for gene expression analysis, ie. most of genes in some thousands of transcripts do not show expression changes. But I'm not sure miRNA expression analysis adopt this hypothesis.
      Last edited by kenosaki; 08-29-2011, 08:20 PM.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Exploring the Dynamics of the Tumor Microenvironment
        by seqadmin




        The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
        07-08-2024, 03:19 PM
      • seqadmin
        Exploring Human Diversity Through Large-Scale Omics
        by seqadmin


        In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
        06-25-2024, 06:43 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 11:09 AM
      0 responses
      18 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 07-19-2024, 07:20 AM
      0 responses
      148 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 07-16-2024, 05:49 AM
      0 responses
      124 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 07-15-2024, 06:53 AM
      0 responses
      111 views
      0 likes
      Last Post seqadmin  
      Working...
      X