Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
EdgeR and Deseq Normalization problems moriah Bioinformatics 4 03-26-2014 04:32 AM
DESeq and edgeR papori Bioinformatics 3 05-15-2012 07:29 PM
EdgeR Normalization Question R_user RNA Sequencing 1 05-07-2012 11:14 PM
edgeR Normalization question polsum Bioinformatics 1 05-07-2012 01:21 AM
Normalization: DESeq vs. EdgeR with method="RLE" aquila RNA Sequencing 3 04-26-2011 10:00 AM

Thread Tools
Old 07-04-2013, 06:27 AM   #1
Location: Finland

Join Date: Aug 2012
Posts: 29
Default edgeR VS deseq normalization


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:

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

normFactor <- calcNormFactors(countTable)
cds <- newCountDataSet(countTable, conditions)
pData(cds)$sizeFactor <- normFactor
Thanks in advance
narges is offline   Reply With Quote

deseq, tmm normalization

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 05:20 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO