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  • narges
    Member
    • Aug 2012
    • 29

    RNA-seq sample clustering using NMF package

    I want to cluster RNA-seq samples (417 samples) using based on the expression levels of a group of selected genes using NMF method. Having a matrix (mat) of expression levels with sample names as columns and gene names as rows I tried following command from Bioconductor NMF package:

    Code:
    library(NMF)
    Code:
    res <- nmf(mat, 2:10, nrun = 200, seed = 123456)
    I figure out that rank=4 is the optimum.
    First do you think it is a reasonable way of sample clustering?
    If so, should I normalize/transform the expression levels before clustering (like TMM normalization or log or asinh transformations)?
    And finally, I need to know the names of samples in each calculated clusters. Using command "basisnames" I got NULL. What command should I try to get the samples orders in clusters?

    Thanks for the help.

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