Header Leaderboard Ad

Collapse

Analyzing miRNA data using MirExpress

Collapse

Announcement

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

  • Analyzing miRNA data using MirExpress

    Hello guys,
    I have to compare two datasets of miRNA sequencing (Illumina data). I installed and ran mirexpress for the two datasets.
    Is there any way to compare the results? I intend to observe the miRNAs differentially expressed between these two datasets. Do I have to normalize the data, or the mirexpress output is already normalized?
    Tahnk you

  • #2
    Based on the information on their site...I have no idea. One possible clue is whether the "expressions" are integers or if they are floating point values. If they are integer then its likely the are raw, unnormalized counts. If they are decimal values then its possible they have been normalized already. It looks like they deal with raw counts and sums of counts so I'd expect the output to be integer and be unnormalized. One would expect the sum of the counts within a sample to be higher for a sample with more reads than for one with fewer reads. Maybe you can test that theory out to see if the data is unnormalized. One more possible check is to plot the expressions against each other. The points should appear to be mostly symmetrical about a 45 degree line projected from (0,0). If he points are obviously shifted to one side or the other then the data is probably not normalized.
    /* Shawn Driscoll, Gene Expression Laboratory, Pfaff
    Salk Institute for Biological Studies, La Jolla, CA, USA */

    Comment


    • #3
      Hello sdriscoll, in fact the values are integers. I tested with other sequence data, and is all the same... Integers.
      I saw something about a R package to work with this. I will take a look and post back some informations.
      Thank you

      Comment

      Latest Articles

      Collapse

      • seqadmin
        How RNA-Seq is Transforming Cancer Studies
        by seqadmin



        Cancer research has been transformed through numerous molecular techniques, with RNA sequencing (RNA-seq) playing a crucial role in understanding the complexity of the disease. Maša Ivin, Ph.D., Scientific Writer at Lexogen, and Yvonne Goepel Ph.D., Product Manager at Lexogen, remarked that “The high-throughput nature of RNA-seq allows for rapid profiling and deep exploration of the transcriptome.” They emphasized its indispensable role in cancer research, aiding in biomarker...
        09-07-2023, 11:15 PM
      • seqadmin
        Methods for Investigating the Transcriptome
        by seqadmin




        Ribonucleic acid (RNA) represents a range of diverse molecules that play a crucial role in many cellular processes. From serving as a protein template to regulating genes, the complex processes involving RNA make it a focal point of study for many scientists. This article will spotlight various methods scientists have developed to investigate different RNA subtypes and the broader transcriptome.

        Whole Transcriptome RNA-seq
        Whole transcriptome sequencing...
        08-31-2023, 11:07 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 09-22-2023, 09:05 AM
      0 responses
      14 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 09-21-2023, 06:18 AM
      0 responses
      12 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 09-20-2023, 09:17 AM
      0 responses
      13 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 09-19-2023, 09:23 AM
      0 responses
      28 views
      0 likes
      Last Post seqadmin  
      Working...
      X