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  • DESeq2 - varianace stabilized pseudocounts and PCA plot

    Hello,

    I am curious to know if:

    1. there is a way to gererate a txt file containing the variance stabilized pseudocounts for each gene,

    2. there is a way to get a table with the x/y coordinates used to produce the PCA plot.

    Thanks in advance for any help.

    Kyle

  • #2
    1. Given a DESeqDataSet named dds, "counts(dds, normalized=T)"
    2. If you just type "plotPCA", you can see that simply using prcomp will produce the raw values that you want (you can also make a modified version of the function to plot arbitrary principal components if you really want).

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