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Old 11-04-2013, 01:06 PM   #1
Junior Member
Location: Baltimore

Join Date: May 2011
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Default DESeq2 - varianace stabilized pseudocounts and PCA plot


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.

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Old 11-05-2013, 02:35 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

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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