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  • katzman
    started a topic DEXSeq cluster heat map like DESeq is desirable

    DEXSeq cluster heat map like DESeq is desirable

    We really like the cluster heat map that we get when using DESeq.

    Is it possible to get a similar plot from DEXSeq?

    This is the code to do it in DESeq:

    Code:
    # need a "full blind" version for variance-stabilized-dispersion heatmap. get it before modifying cds
    fullBlind.method      <- "blind"
    fullBlind.sharingMode <- "fit-only"
    fullBlind.fitType     <- "local"
    cdsFullBlind <- estimateDispersions(cds, method=fullBlind.method, sharingMode=fullBlind.sharingMode, fitType=fullBlind.fitType  )
    # per the vignette, should use "blind" dispersion estimates to avoid bias
    vsd <- getVarianceStabilizedData(cdsFullBlind)
    dists <- dist( t(vsd) )
    heatmap (as.matrix(dists), symm=TRUE)

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