Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • narges
    Member
    • Aug 2012
    • 29

    #1

    edgeR VS deseq normalization

    Hi,

    I intend to run RNA-seq analysis using DESeq package. But since I am working on TMM normalization method I wanted to run DESeq with TMM as well. I wanted to ask if it is enough if I pass the "norm.factors" obtained from "calcNormFactors" from edgeR to "sizeFactor" of DESeq. Or I should multiply the "norm.factors" by library size and then passed it to DESeq?
    Or do you think it is meaningful or not?
    So either of these:

    Code:
    normFactor <- calcNormFactors(countTable)
    scale <- countTable$samples$lib.size*countTable$samples$norm.factors
    cds <- newCountDataSet(countTable, conditions)
    pData(cds)$sizeFactor <- scale
    OR:

    Code:
    normFactor <- calcNormFactors(countTable)
    cds <- newCountDataSet(countTable, conditions)
    pData(cds)$sizeFactor <- normFactor
    Thanks in advance

Latest Articles

Collapse

  • kinpict.com
    Reply to 16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
    by kinpict.com
    The part about this topic feels surprisingly grounded, and the details on the page is the bit that made me slow down. I’d keep <a href="https://kinpict.com/">ai family photo generator</a> bookmarked for later.
    Today, 06:37 PM
  • SEQadmin2
    16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
    by SEQadmin2





    NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...
    10-30-2026, 06:46 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, 11-12-2026, 07:59 AM
0 responses
27 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 11-05-2026, 09:25 AM
0 responses
35 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 11-03-2026, 11:54 AM
2 responses
56 views
0 reactions
Last Post kinpict.com  
Started by SEQadmin2, 10-28-2026, 09:57 AM
0 responses
175 views
0 reactions
Last Post SEQadmin2  
Working...