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  • #1

    TMM nomalization in RNA-seq

    could anyone tell me that what's mean of Sk in TMM? how can i get the method in a simple way?
    Tags: None
  • #2
    Hi minghui.

    I'm actually not sure what you mean by 'mean of Sk'? Can you clarify?

    The procedure is implemented in the Bioconductor edgeR package ... see the calcNormFactors() function:
    edgeR
    http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
    Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce read counts, including ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE and CAGE.


    Cheers,
    Mark

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