Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • RNA-Seq: Length Bias Correction for RNA-seq Data in Gene Set Analyses.

    Syndicated from PubMed RSS Feeds

    Length Bias Correction for RNA-seq Data in Gene Set Analyses.

    Bioinformatics. 2011 Jan 19;

    Authors: Gao L, Fang Z, Zhang K, Zhi D, Cui X

    MOTIVATION: Next-generation sequencing technology is being rapidly applied to quantifying transcripts (RNA-seq). However, due to the unique properties of the RNA-seq data, the differential expression of longer transcripts is more likely to be identified than that of shorter transcripts with the same effect size. This bias complicates the downstream gene set analysis (GSA) because the methods for GSA previously developed for microarray data are based on the assumption that genes with same effect size have equal probability (power) to be identified as significantly differentially expressed. Since transcript length is not related to gene expression, adjusting for such length dependency in GSA becomes necessary. RESULTS: In this paper, we proposed two approaches for transcript-length adjustment for analyses based on Poisson models: 1) At individual gene level, we adjusted each gene's test statistic using the square root of transcript length followed by testing for gene set using the Wilcoxon Rank-Sum test. 2) At gene-set level, we adjusted the null distribution for the Fisher's exact test by weighting the identification probability of each gene using the square root of its transcript length. We evaluated these two approaches using simulations and a real dataset, and showed that these methods can effectively reduce the transcript-length biases. The top ranked GO terms obtained from the proposed adjustments show more overlaps with the microarray results. AVAILABILITY: R scripts are at http://www.soph.uab.edu/Statgenetics.../XCui/r-codes/ CONTACT: [email protected].

    PMID: 21252076 [PubMed - as supplied by publisher]



    More...

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
7 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
7 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
49 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
66 views
0 likes
Last Post seqadmin  
Working...
X