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  • minghui
    Junior Member
    • Feb 2010
    • 7

    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?
  • markrobinsonca
    Junior Member
    • Mar 2010
    • 7

    #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:
    Differential expression analysis of sequence count data. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models, quasi-likelihood, and gene set enrichment. Can perform differential analyses of any type of omics data that produces read counts, including RNA-seq, ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE, CAGE, metabolomics, or proteomics spectral counts. RNA-seq analyses can be conducted at the gene or isoform level, and tests can be conducted for differential exon or transcript usage.


    Cheers,
    Mark

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