DESeq2 - varianace stabilized pseudocounts and PCA plot

[KHubbard]

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

[dpryan]

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).