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  • 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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