Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • The standard way to normalize eQTL expression data?

    Recently I found some papers normalized RNA-seq/Microarray gene expression matrix for following eQTL mapping like this:
    First quantile normalize across samples, then centered and standardized for each gene (usually by subtracting median and divided by standard deviation).
    I'm not sure the assumption underlying this normalization approach. After centering and standardization, every gene has 0 mean and 1 sd, but in common sense some genes must have high variance across samples, and there are genes stably expressed and so have less variance. SO, why we should make the variance the same?
    Moreover, if we want to apply some following analysis like MDS, PCA or ICA to remove batch effects or confounding factors in raw expression data, is it right to normalize data like that? OR, the normalization method used depends on personal preference. Is there a standard way? Thank you so much for your advice !


    There is also a paper centered and standardized for each sample rather than for each gene! I'm more confused.
    Last edited by beliefbio; 05-14-2012, 09:08 AM.

Latest Articles

Collapse

  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM
  • 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

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
30 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
32 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
28 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
52 views
0 likes
Last Post seqadmin  
Working...
X