Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • hollandorange
    Member
    • May 2010
    • 11
    #1

    Cuffdiff on two sample RNA-Seq

    Hi All,

    I have two RNA-Seq samples: 1 control and 1 disease. And I apply Cuffdiff to detect the differentially expressed genes. And here are questions:

    (1) since there are only two samples. does the p-value or q-value still make sense?

    (2) I noticed that if a gene is express in one sample (for example FRKMa=10) but not in the other one (FRKMb=0), then it is not significant according to the p-value. Is it always true? There are about 2k this kind of genes, how to handle them?

    Best wishes
    Yanju
    Tags: None
  • NicoBxl
    not just another member
    • Aug 2010
    • 264
    #2
    (1) no. only one sample per group is not statistically enough. you can not conclude anything with this type of experiment.

    (2) yes it's normal that you're p-val is not significant with two sample. even if the difference between the two FPKM is big.

    Comment

    Previous template Next

    Latest Articles

    Collapse
    • SEQadmin2
      Nine Things a Sample Prep Scientist Thinks About Before Sequencing
      by SEQadmin2


      I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

      Here are nine questions we think about, in roughly the order they matter, before...
      06-18-2026, 07:11 AM
    • SEQadmin2
      From Collection to Sequencing: Why Sample Preparation and Preservation Define Sequencing Data
      by SEQadmin2


      Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.

      The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
      ...
      06-02-2026, 10:05 AM
    View All

    ad_right_rmr

    Collapse

    News

    Collapse
    Topics Statistics Last Post
    Large-Scale Protein Screen Uncovers Hidden Regulators of Alternative Polyadenylation by SEQadmin2
    Started by SEQadmin2, 06-26-2026, 11:10 AM
    0 responses
    11 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    06-26-2026, 11:10 AM  
    Whole-Genome Sequencing Traces Faroe Islands Ancestry to a North Atlantic Founder Population by SEQadmin2
    Started by SEQadmin2, 06-17-2026, 06:09 AM
    0 responses
    46 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    06-17-2026, 06:09 AM  
    Sequencing the Two-Toed Sloth Genome Reveals Jumping Genes Tied to Its Extreme Metabolism by SEQadmin2
    Started by SEQadmin2, 06-09-2026, 11:58 AM
    0 responses
    105 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    06-09-2026, 11:58 AM  
    A New Method Makes Hantavirus Genome Analysis Faster and More Accessible by SEQadmin2
    Started by SEQadmin2, 06-05-2026, 10:09 AM
    0 responses
    125 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    06-05-2026, 10:09 AM  
    View All
    Working...