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Old 07-04-2013, 05:27 AM   #1
narges
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Location: Finland

Join Date: Aug 2012
Posts: 29
Default 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
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