What are ntop on plotPCA vsd in DESeq2?
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Entering edit mode
2.2 years ago
ecg1g15 ▴ 30

I am trying to understand the following DESeq PCA code:

plotPCA(vsd, intgroup = "condition", ntop = 500)

VERY different to the differentially expressed subset of genes from here:

de <- rownames(res[res$padj<0.05 & !is.na(res$padj), ]) 

plotPCA(vsd[de,], intgroup = "condition", ntop = 500)

What are thos ntop=500 selected at the beginning then? based on what are they TOP?

DESeq2 RNA-Seq R PCA plotPCA • 1.7k views
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Entering edit mode
2.2 years ago
ATpoint 68k

Please read the help ?DESeq2::plotPCA

ntop: number of top genes to use for principal components, selected by highest row variance

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