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  • markrobinsonca
    replied
    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:
    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

    Leave a comment:


  • minghui
    started a topic TMM nomalization in RNA-seq

    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?

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