Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • lynn012
    Junior Member
    • Sep 2010
    • 9
    #1

    How to calculate P-value&FDR

    Hi,
    When I analyse the significance of gene expression profiles, I should calculate the P-value&FDR. But I don't know how to calculate.Grateful for answers.
    Thanks!
    Tags: None
  • dariober
    Senior Member
    • May 2010
    • 311
    #2
    Originally posted by lynn012 View Post
    Hi,
    When I analyse the significance of gene expression profiles, I should calculate the P-value&FDR. But I don't know how to calculate.Grateful for answers.
    Thanks!
    Hi,

    If you are talking about a microarray experiment have a look at the R/Bioconductor package limma. If it is next gen data (RNAseq, Chipseq) see the packages edger or deseq. If instead you want to convert a vector of p-values to fdr values see the function p.adjust in R.

    (A suggestion... I think you should make your questions a bit more detailed for people to help!)

    Dario

    Comment

    • lynn012
      Junior Member
      • Sep 2010
      • 9
      #3
      Dario,
      Thanks for your help and I will make my questions a bit more detailed in the future. My data is next gen data(DGE). Thanks for your timely answer and patient explaination again!

      Comment

      Previous template Next

      Latest Articles

      Collapse
      • SEQadmin2
        Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems
        by SEQadmin2



        Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
        ...
        07-09-2026, 11:10 AM
      • SEQadmin2
        Cancer Drug Resistance: The Lingering Barrier to Rising Survival
        by SEQadmin2



        Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.

        There is no single reason why many patients don’t respond to treatment as expected. Cancer is...
        07-08-2026, 05:17 AM
      • GATTACAT
        Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing
        by GATTACAT
        Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
        07-01-2026, 11:43 AM
      View All

      ad_right_rmr

      Collapse

      News

      Collapse
      Topics Statistics Last Post
      New Analysis Splits Leukemia Into 16 Epigenomic Subgroups by SEQadmin2
      Started by SEQadmin2, 07-09-2026, 10:04 AM
      0 responses
      24 views
      0 reactions
      		 Last Post SEQadmin2
      by SEQadmin2
      07-09-2026, 10:04 AM  
      Genome-Wide CRISPR Screen Uncovers Unlikely Psoriasis Target by SEQadmin2
      Started by SEQadmin2, 07-08-2026, 10:08 AM
      0 responses
      15 views
      0 reactions
      		 Last Post SEQadmin2
      by SEQadmin2
      07-08-2026, 10:08 AM  
      Engineered Protein Motor Takes Its First Steps Along DNA Track by SEQadmin2
      Started by SEQadmin2, 07-07-2026, 11:05 AM
      0 responses
      33 views
      0 reactions
      		 Last Post SEQadmin2
      by SEQadmin2
      07-07-2026, 11:05 AM  
      High-Resolution Sequencing Exposes Hidden Toxoplasma Diversity by SEQadmin2
      Started by SEQadmin2, 07-02-2026, 11:08 AM
      0 responses
      31 views
      0 reactions
      		 Last Post SEQadmin2
      by SEQadmin2
      07-02-2026, 11:08 AM  
      View All
      Working...